1
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Hsu FM, Chang YL, Chen CY, Lin SR, Cheng JCH. Hybridization Protection Reaction for Sensitive and Robust Gene Expression Profiling of Clinical Formalin-Fixed Paraffin-Embedded Samples. Clin Chem 2023; 69:1385-1395. [PMID: 37964418 DOI: 10.1093/clinchem/hvad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/03/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND RNA profiling of formalin-fixed paraffin-embedded (FFPE) tumor tissues for the molecular diagnostics of disease prognosis or treatment response is often irreproducible and limited to a handful of biomarkers. This has led to an unmet need for robust multiplexed assays that can profile several RNA biomarkers of interest using a limited amount of specimen. Here, we describe hybridization protection reaction (HPR), which is a novel RNA profiling approach with high reproducibility. METHODS HPR assays were designed for multiple genes, including 10 radiosensitivity-associated genes, and compared with TaqMan assays. Performance was tested with synthetic RNA fragments, and the ability to analyze RNA was investigated in FPPE samples from 20 normal lung tissues, 40 lung cancer, and 30 esophageal cancer biopsies. RESULTS Experiments performed on 3 synthetic RNA fragments demonstrated a linear dynamic range of over 1000-fold with a replicate correlation coefficient of 0.99 and high analytical sensitivity between 3.2 to 10 000 pM. Comparison of HPR with standard quantitative reverse transcription polymerase chain reaction on FFPE specimens shows nonsignificant differences with > 99% confidence interval between 2 assays in transcript profiling of 91.7% of test transcripts. In addition, HPR was effectively applied to quantify transcript levels of 10 radiosensitivity-associated genes. CONCLUSIONS Overall, HPR is an alternative approach for RNA profiling with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
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Affiliation(s)
- Feng-Ming Hsu
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yih-Leong Chang
- Department of Pathology, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Shu-Rung Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Jason Chia-Hsien Cheng
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
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2
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Huang X, Zhao W, Chen X, Li J, Ye H, Li C, Yin X, Zhou X, Qiao X, Xue Z, Wang T. Gold Nanoparticle-Bridge Array to Improve DNA Hybridization Efficiency of SERS Sensors. J Am Chem Soc 2022; 144:17533-17539. [PMID: 36000980 DOI: 10.1021/jacs.2c06623] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interfacial mass transfer rate of a target has a significant impact on the sensing performance. The surface reaction forms a concentration gradient perpendicular to the surface, wherein a slow mass transfer process decreases the interfacial reaction rate. In this work, we self-assembled gold nanoparticles (AuNPs) in the gap of a SiO2 opal array to form a AuNP-bridge array. The diffusion paths of vertical permeability and a microvortex effect provided by the AuNP-bridge array synergistically improved the target mass transfer efficiency. As a proof of concept, we used DNA hybridization efficiency as a research model, and the surface-enhanced Raman spectroscopy (SERS) signal acted as a readout index. The experimental verification and theoretical simulation show that the AuNP-bridge array exhibited rapid mass transfer and high sensitivity. The DNA hybridization efficiency of the AuNP-bridge array was 15-fold higher than that of the AuNP-planar array. We believe that AuNP-bridge arrays can be potentially applied for screening drug candidates, genetic variations, and disease biomarkers.
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Affiliation(s)
- Xiaobin Huang
- Tianjin Key Laboratory of Drug Targeting and Bioimaging, Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin 300384, P. R. China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,School of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Weidong Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xiangyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jinming Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Haochen Ye
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Cancan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xiaomeng Yin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xinyuan Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xuezhi Qiao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Zhenjie Xue
- Tianjin Key Laboratory of Drug Targeting and Bioimaging, Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin 300384, P. R. China
| | - Tie Wang
- Tianjin Key Laboratory of Drug Targeting and Bioimaging, Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin 300384, P. R. China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,School of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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3
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Vanjur L, Carzaniga T, Casiraghi L, Zanchetta G, Damin F, Sola L, Chiari M, Buscaglia M. Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization. Polymers (Basel) 2021; 13:polym13223897. [PMID: 34833198 PMCID: PMC8625010 DOI: 10.3390/polym13223897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
The physical–chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal’s amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-mer DNA, when the probe strands are immobilized on different copolymers, which coat the surface of an optical, label-free biosensor. Copolymers of N, N-dimethylacrylamide bringing either a different type or density of sites for covalent immobilization of DNA probes, or different backbone charges, were used to functionalize the surface of a Reflective Phantom Interface multispot biosensor made of a glass prism with a silicon dioxide antireflective layer. By analyzing the kinetic hybridization curves at different probe surface densities and target concentrations in solution, we found that all the tested coatings displayed a common association kinetics of about 9 × 104 M−1·s−1 at small probe density, decreasing by one order of magnitude close to the surface saturation of probes. In contrast, both the yield of hybridization and the dissociation kinetics, and hence the equilibrium constant, depend on the type of copolymer coating. Nearly doubled signal amplitudes, although equilibrium dissociation constant was as large as 4 nM, were obtained by immobilizing the probe via click chemistry, whereas amine-based immobilization combined with passivation with diamine carrying positive charges granted much slower dissociation kinetics, yielding an equilibrium dissociation constant as low as 0.5 nM. These results offer quantitative criteria for an optimal selection of surface copolymer coatings, depending on the application.
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Affiliation(s)
- Luka Vanjur
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche, Consiglio Nazionale delle Ricerche (CNR-SCITEC), 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Laura Sola
- Istituto di Scienze e Tecnologie Chimiche, Consiglio Nazionale delle Ricerche (CNR-SCITEC), 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche, Consiglio Nazionale delle Ricerche (CNR-SCITEC), 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
- Correspondence: ; Tel.: +39-0250330352
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4
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Vanjur L, Carzaniga T, Casiraghi L, Chiari M, Zanchetta G, Buscaglia M. Non-Langmuir Kinetics of DNA Surface Hybridization. Biophys J 2020; 119:989-1001. [PMID: 32738217 PMCID: PMC7474173 DOI: 10.1016/j.bpj.2020.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/10/2020] [Accepted: 07/21/2020] [Indexed: 01/12/2023] Open
Abstract
Hybridization of complementary single strands of DNA represents a very effective natural molecular recognition process widely exploited for diagnostic, biotechnology, and nanotechnology applications. A common approach relies on the immobilization on a surface of single-stranded DNA probes that bind complementary targets in solution. However, despite the deep knowledge on DNA interactions in bulk solution, the modeling of the same interactions on a surface are still challenging and perceived as strongly system dependent. Here, we show that a two-dimensional analysis of the kinetics of hybridization, performed at different target concentrations and probe surface densities by a label-free optical biosensor, reveals peculiar features inconsistent with an ideal Langmuir-like behavior. We propose a simple non-Langmuir kinetic model accounting for an enhanced electrostatic repulsion originating from the surface immobilization of nucleic acids and for steric hindrance close to full hybridization of the surface probes. The analysis of the kinetic data by the model enables quantifying the repulsive potential at the surface, as well as retrieving the kinetic parameters of isolated probes. We show that the strength and the kinetics of hybridization at large probe density can be improved by a three-dimensional immobilization strategy of probe strands with a double-stranded linker.
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Affiliation(s)
- Luka Vanjur
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy.
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5
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Yang P, Li Y, Mason SD, Chen F, Chen J, Zhou R, Liu J, Hou X, Li F. Concentric DNA Amplifier That Streamlines In-Solution Biorecognition and On-Particle Biocatalysis. Anal Chem 2020; 92:3220-3227. [PMID: 31957445 DOI: 10.1021/acs.analchem.9b04964] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Colloidal nanoparticle biosensors capable of on-particle biocatalysis are powerful tools for amplified detection of biomolecules. The development and practical uses of such concentric amplifiers can be complicated because of the on-particle biorecognition that involves varying interfacial factors at the biomolecule-nanoparticle interfaces. Herein, we reason that a nanoparticle biosensor equipped with an in-solution biorecognition element may be better fabricated, predicted, controlled, and performed. The in-solution biorecognition shall also be streamlined with the on-particle biocatalysis so that the overall analytical and kinetic performance is not compromised. As a testbed, we introduce a concentric DNA amplifier driven by an enzyme-powered three-dimensional DNA nanomachine, where a DNA walker can be instantly assembled onto a spherical nucleic acid (SNA) track through a polyadenosine anchor. As such, the free DNA walker can participate in reactions in a homogeneous solution before assembling to the SNA track. The instant and stable assembly enabled by both adsorption and complementary base pairing also ensures rapid on-particle biocatalysis. We demonstrate that the in-solution biorecognition effectively eliminates the binding hindrance encountered by the on-particle biorecognition and thus significantly reduced energy barriers for the detection of nucleic acids and proteins. Because of the in-solution biorecognition, our system can also be plugged readily into complex DNA strand displacement networks for rapid signal amplification.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan 610064 , China.,Department of Chemistry, Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada.,Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yongya Li
- Department of Chemistry, Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
| | - Sean D Mason
- Department of Chemistry, Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
| | - Fangfang Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan 610064 , China.,Department of Chemistry, Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
| | - Junbo Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan 610064 , China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital , Sichuan University , Chengdu , Sichuan 610064 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Xiandeng Hou
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan 610064 , China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan 610064 , China.,Department of Chemistry, Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
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6
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Duffy J, Padovani F, Brunetti G, Noy P, Certa U, Hegner M. Towards personalised rapid label free miRNA detection for cancer and liver injury diagnostics in cell lysates and blood based samples. NANOSCALE 2018; 10:12797-12804. [PMID: 29947396 DOI: 10.1039/c8nr03604g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Advances in prevention, diagnosis and therapy are coupled to innovation and development of new medical tools, leading to improved patient prognosis. We developed an automatic biosensor platform that could provide a non-invasive, rapid and personalised diagnosis using nanomechanical cantilever sensors. miRNA are involved in gene expression and are extractable biomarkers for multiple diseases. We detected specific expression patterns of miRNA relevant to cancer and adverse drug effects directly in cell lysates or blood based samples using only a few microliters of sample within one hour. Specific miRNA hybridisation to the upper cantilever surface induces physical bending of the sensor which is detected by monitoring the position of a laser that reflects from the sensors surface. Internal reference sensors negate environmental and nonspecific effects. We showed that the sensitivity of label free cantilever nanomechanical sensing of miRNA surpasses that of surface plasmon resonance by more than three orders of magnitude. A cancer associated miRNA expression profile from cell lysates and one associated with hepatocytes derived from necrotic liver tissue in blood-based samples has been successfully detected. Our label free mechanical approach displays the capability to perform in relevant clinical samples while also obtaining comparable results to PCR based techniques. Without the need to individually extend, amplify or label each target allowing multitarget analysis from one sample.
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Affiliation(s)
- James Duffy
- Centre Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin 2, Ireland.
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7
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Montis C, Generini V, Boccalini G, Bergese P, Bani D, Berti D. Model lipid bilayers mimic non-specific interactions of gold nanoparticles with macrophage plasma membranes. J Colloid Interface Sci 2018; 516:284-294. [DOI: 10.1016/j.jcis.2018.01.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/17/2018] [Accepted: 01/18/2018] [Indexed: 12/31/2022]
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8
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Interaction of Extracellular Vesicles with Si Surface Studied by Nanomechanical Microcantilever Sensors. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8030404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Rodriguez-Quijada C, Sánchez-Purrà M, de Puig H, Hamad-Schifferli K. Physical Properties of Biomolecules at the Nanomaterial Interface. J Phys Chem B 2018; 122:2827-2840. [DOI: 10.1021/acs.jpcb.8b00168] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | - Maria Sánchez-Purrà
- Department of Engineering, University of Massachusetts, Boston, Massachusetts 02125, United States
| | - Helena de Puig
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kimberly Hamad-Schifferli
- Department of Engineering, University of Massachusetts, Boston, Massachusetts 02125, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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Montis C, Busatto S, Valle F, Zendrini A, Salvatore A, Gerelli Y, Berti D, Bergese P. Biogenic Supported Lipid Bilayers from Nanosized Extracellular Vesicles. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201700200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Costanza Montis
- Department of Chemistry; University of Florence and CSGI; via della Lastruccia 3 50019 Florence Italy
| | - Sara Busatto
- Department of Molecular and Translational Medicine; University of Brescia; CSGI and INSTM, viale Europa 11 25123 Brescia Italy
| | | | - Andrea Zendrini
- Department of Molecular and Translational Medicine; University of Brescia; CSGI and INSTM, viale Europa 11 25123 Brescia Italy
| | - Annalisa Salvatore
- Department of Chemistry; University of Florence and CSGI; via della Lastruccia 3 50019 Florence Italy
| | - Yuri Gerelli
- Institut Laue-Langevin; 71 Avenue des Martyrs BP 156 F-38000 Grenoble France
| | - Debora Berti
- Department of Chemistry; University of Florence and CSGI; via della Lastruccia 3 50019 Florence Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine; University of Brescia; CSGI and INSTM, viale Europa 11 25123 Brescia Italy
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11
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Berto M, Diacci C, D'Agata R, Pinti M, Bianchini E, Lauro MD, Casalini S, Cossarizza A, Berggren M, Simon D, Spoto G, Biscarini F, Bortolotti CA. EGOFET Peptide Aptasensor for Label-Free Detection of Inflammatory Cytokines in Complex Fluids. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700072] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Marcello Berto
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Chiara Diacci
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche; Università di Catania; V.le A. Doria 6 95131 Catania
| | - Marcello Pinti
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Elena Bianchini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Michele Di Lauro
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Stefano Casalini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Andrea Cossarizza
- Dipartimento di Scienze Mediche e Chirurgiche Materno-Infantili e dell'Adulto; Università di Modena e Reggio Emilia; Via Campi 287 41125 Modena Italy
| | - Magnus Berggren
- Laboratory of Organic Electronics; Department of Science and Technology; ITN; Linköping University; S-601 74 Norrköping Sweden
| | - Daniel Simon
- Laboratory of Organic Electronics; Department of Science and Technology; ITN; Linköping University; S-601 74 Norrköping Sweden
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche; Università di Catania; V.le A. Doria 6 95131 Catania
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici; c/o Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6 95131 Catania Italy
| | - Fabio Biscarini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Carlo A. Bortolotti
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
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12
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Label-free detection of interleukin-6 using electrolyte gated organic field effect transistors. Biointerphases 2017; 12:05F401. [PMID: 28954519 DOI: 10.1116/1.4997760] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cytokines are small proteins that play fundamental roles in inflammatory processes in the human body. In particular, interleukin (IL)-6 is a multifunctional cytokine, whose increased levels are associated with infection, cancer, and inflammation. The quantification of IL-6 is therefore of primary importance in early stages of inflammation and in chronic diseases, but standard techniques are expensive, time-consuming, and usually rely on fluorescent or radioactive labels. Organic electronic devices and, in particular, organic field-effect transistors (OFETs) have been proposed in the recent years as novel platforms for label-free protein detection, exploiting as sensing unit surface-immobilized antibodies or aptamers. Here, the authors report two electrolyte-gated OFETs biosensors for IL-6 detection, featuring monoclonal antibodies and peptide aptamers adsorbed at the gate. Both strategies yield biosensors that can work on a wide range of IL-6 concentrations and exhibit a remarkable limit of detection of 1 pM. Eventually, electrolyte gated OFETs responses have been used to extract and compare the binding thermodynamics between the sensing moiety, immobilized at the gate electrode, and IL-6.
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13
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Manoli K, Magliulo M, Mulla MY, Singh M, Sabbatini L, Palazzo G, Torsi L. Druckbare Bioelektronik zur Untersuchung funktioneller biologischer Grenzflächen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Manoli K, Magliulo M, Mulla MY, Singh M, Sabbatini L, Palazzo G, Torsi L. Printable Bioelectronics To Investigate Functional Biological Interfaces. Angew Chem Int Ed Engl 2015; 54:12562-76. [DOI: 10.1002/anie.201502615] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Indexed: 01/14/2023]
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15
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Mulla MY, Tuccori E, Magliulo M, Lattanzi G, Palazzo G, Persaud K, Torsi L. Capacitance-modulated transistor detects odorant binding protein chiral interactions. Nat Commun 2015; 6:6010. [PMID: 25591754 PMCID: PMC4309438 DOI: 10.1038/ncomms7010] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/02/2014] [Indexed: 12/25/2022] Open
Abstract
Peripheral events in olfaction involve odorant binding proteins (OBPs) whose role in the recognition of different volatile chemicals is yet unclear. Here we report on the sensitive and quantitative measurement of the weak interactions associated with neutral enantiomers differentially binding to OBPs immobilized through a self-assembled monolayer to the gate of an organic bio-electronic transistor. The transduction is remarkably sensitive as the transistor output current is governed by the small capacitance of the protein layer undergoing minute changes as the ligand-protein complex is formed. Accurate determination of the free-energy balances and of the capacitance changes associated with the binding process allows derivation of the free-energy components as well as of the occurrence of conformational events associated with OBP ligand binding. Capacitance-modulated transistors open a new pathway for the study of ultra-weak molecular interactions in surface-bound protein-ligand complexes through an approach that combines bio-chemical and electronic thermodynamic parameters.
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Affiliation(s)
- Mohammad Yusuf Mulla
- Dipartimento di Chimica and CSGI, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
| | - Elena Tuccori
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, UK
| | - Maria Magliulo
- Dipartimento di Chimica and CSGI, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
| | - Gianluca Lattanzi
- Dipartimento di Fisica ‘M. Merlin’, INFN and TIRES, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
| | - Gerardo Palazzo
- Dipartimento di Chimica and CSGI, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
| | - Krishna Persaud
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, UK
| | - Luisa Torsi
- Dipartimento di Chimica and CSGI, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
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16
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Biavardi E, Federici S, Tudisco C, Menozzi D, Massera C, Sottini A, Condorelli GG, Bergese P, Dalcanale E. Cavitand-Grafted Silicon Microcantilevers as a Universal Probe for Illicit and Designer Drugs in Water. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Biavardi E, Federici S, Tudisco C, Menozzi D, Massera C, Sottini A, Condorelli GG, Bergese P, Dalcanale E. Cavitand-grafted silicon microcantilevers as a universal probe for illicit and designer drugs in water. Angew Chem Int Ed Engl 2014; 53:9183-8. [PMID: 24909594 DOI: 10.1002/anie.201404774] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 02/04/2023]
Abstract
The direct, clean, and unbiased transduction of molecular recognition into a readable and reproducible response is the biggest challenge associated to the use of synthetic receptors in sensing. All possible solutions demand the mastering of molecular recognition at the solid-liquid interface as prerequisite. The socially relevant issue of screening amine-based illicit and designer drugs is addressed by nanomechanical recognition at the silicon-water interface. The methylamino moieties of different drugs are all first recognized by a single cavitand receptor through a synergistic set of weak interactions. The peculiar recognition ability of the cavitand is then transferred with high fidelity and robustness on silicon microcantilevers and harnessed to realize a nanomechanical device for label-free detection of these drugs in water.
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Affiliation(s)
- Elisa Biavardi
- Dipartimento di Chimica, Università degli Studi di Parma and INSTM Udr Parma, Parco Area delle Scienze 17A, 43124 Parma (Italy)
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18
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Maiolo D, Mitola S, Leali D, Oliviero G, Ravelli C, Bugatti A, Depero LE, Presta M, Bergese P. Role of nanomechanics in canonical and noncanonical pro-angiogenic ligand/VEGF receptor-2 activation. J Am Chem Soc 2012; 134:14573-9. [PMID: 22860754 DOI: 10.1021/ja305816p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR2) is an endothelial cell receptor that plays a pivotal role in physiologic and pathologic angiogenesis and is a therapeutic target for angiogenesis-dependent diseases, including cancer. By leveraging on a dedicated nanomechanical biosensor, we investigated the nanoscale mechanical phenomena intertwined with VEGFR2 surface recognition by its prototypic ligand VEGF-A and its noncanonical ligand gremlin. We found that the two ligands bind the immobilized extracellular domain of VEGFR2 (sVEGFR2) with comparable binding affinity. Nevertheless, they interact with sVEGFR2 with different binding kinetics and drive different in-plane piconewton intermolecular forces, suggesting that the binding of VEGF-A or gremlin induces different conformational changes in sVEGFR2. These behaviors can be effectively described in terms of a different "nanomechanical affinity" of the two ligands for sVEGFR2, about 16-fold higher for VEGF-A with respect to gremlin. Such nanomechanical differences affect the biological activity driven by the two angiogenic factors in endothelial cells, as evidenced by a more rapid VEGFR2 clustering and a more potent mitogenic response triggered by VEGF-A in respect to gremlin. Together, these data point to surface intermolecular interactions on cell membrane between activated receptors as a key modulator of the intracellular signaling cascade.
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Affiliation(s)
- Daniele Maiolo
- Chemistry for Technologies Laboratory and INSTM, School of Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
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19
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Federici S, Oliviero G, Maiolo D, Depero LE, Colombo I, Bergese P. On the thermodynamics of biomolecule surface transformations. J Colloid Interface Sci 2012; 375:1-11. [DOI: 10.1016/j.jcis.2012.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 02/06/2023]
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20
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Dionisio M, Oliviero G, Menozzi D, Federici S, Yebeutchou RM, Schmidtchen FP, Dalcanale E, Bergese P. Nanomechanical Recognition of N-Methylammonium Salts. J Am Chem Soc 2012; 134:2392-8. [DOI: 10.1021/ja210567k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Dionisio
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Giulio Oliviero
- Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123 Brescia,
Italy
| | - Daniela Menozzi
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Stefania Federici
- Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123 Brescia,
Italy
| | - Roger M. Yebeutchou
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | | | - Enrico Dalcanale
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Paolo Bergese
- Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123 Brescia,
Italy
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21
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de Puig H, Federici S, Baxamusa SH, Bergese P, Hamad-Schifferli K. Quantifying the nanomachinery of the nanoparticle-biomolecule interface. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2477-84. [PMID: 21692181 DOI: 10.1002/smll.201100530] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 05/21/2023]
Abstract
A study is presented of the nanomechanical phenomena experienced by nanoparticle-conjugated biomolecules. A thermodynamic framework is developed to describe the binding of thrombin-binding aptamer (TBA) to thrombin when the TBA is conjugated to nanorods. Binding results in nanorod aggregation (viz. directed self-assembly), which is detectable by absorption spectroscopy. The analysis introduces the energy of aggregation, separating it into TBA-thrombin recognition and surface-work contributions. Consequently, it is demonstrated that self-assembly is driven by the interplay of surface work and thrombin-TBA recognition. It is shown that the work at the surface is about -10 kJ mol(-1) and results from the accumulation of in-plane molecular forces of pN magnitude and with a lifetime of <1 s, which arises from TBA nanoscale rearrangements fuelled by thrombin-directed nanorod aggregation. The obtained surface work can map aggregation regimes as a function of different nanoparticle surface conditions. Also, the thermodynamic treatment can be used to obtain quantitative information on surface effects impacting biomolecules on nanoparticle surfaces.
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Affiliation(s)
- Helena de Puig
- Department of Biological Engineering and the Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA; Institut Quimic de Sarrià, Universitat Ramon Llull Via Augusta 390, 08017 Barcelona, Spain
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