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Nava G, Casiraghi L, Carzaniga T, Zanchetta G, Chiari M, Damin F, Bollati V, Signorini L, Delbue S, Bellini T, Buscaglia M. Digital Detection of Single Virus Particles by Multi-Spot, Label-Free Imaging Biosensor on Anti-Reflective Glass. Small 2023; 19:e2300947. [PMID: 37060208 DOI: 10.1002/smll.202300947] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Rapid detection of whole virus particles in biological or environmental samples represents an unmet need for the containment of infectious diseases. Here, an optical device enabling the enumeration of single virion particles binding on antibody or aptamers immobilized on a surface with anti-reflective coating is described. In this regime, nanoparticles adhering to the sensor surface provide localized contributions to the reflected field that become detectable because of their mixing with the interfering waves in the reflection direction. Thus, these settings are exploited to realize a scan-free, label-free, micro-array-type digital assay on a disposable cartridge, in which the virion counting takes place in wide field-of-view imaging. With this approach we could quantify, by enumeration, different variants of SARS-CoV-2 virions interacting with antibodies and aptamers immobilized on different spots. For all tested variants, the aptamers showed larger affinity but lower specificity relative to the antibodies. It is found that the combination of different probes on the same surface enables increasing specificity of detection and dynamic range.
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Affiliation(s)
- Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, Milano, 20131, Italy
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, Milano, 20131, Italy
| | - Valentina Bollati
- Dipartimento di Scienze Cliniche e di Comunitá, Universitá degli Studi di Milano, via S. Barnaba 8, Milano, 20122, Italy
| | - Lucia Signorini
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Universitá degli Studi di Milano, via Pascal 36, Milano, 20133, Italy
| | - Serena Delbue
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Universitá degli Studi di Milano, via Pascal 36, Milano, 20133, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
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Brambilla D, Sola L, Damin F, Mussida A, Chiari M. Immobilization of biotinylated antibodies through streptavidin binding aptamer. Talanta 2023; 265:124847. [PMID: 37390669 DOI: 10.1016/j.talanta.2023.124847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023]
Abstract
Liquid biopsy approaches are powerful strategies that potentially allow the diagnosis and prognosis of a number of diseases. The field is continuously and rapidly growing, encouraging the discovery of novel predictory biomarkers. Antibodies are usually exploited in sensors to validate biomarker candidates. Unfortunately, the immobilization of antibodies on the surface of sensors represents a challenging task. Immobilization strategies need to be optimized for each antibody, representing a huge obstacle to overcome in the discovery of new biomarkers. Herein we propose a novel strategy for the immobilization of antibodies, based on the use of a streptavidin-binding aptamer. Using this approach it is possible to immobilize antibodies on the surface of sensors with no need for optimization, with the only requirement for antibody to be biotinylated. The proposed strategy potentially paves the way towards a straightforward immobilization of antibodies on biosensors, making their use in biomarker validation more accessible.
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Affiliation(s)
- D Brambilla
- National Research Council of Italy - Institute of Chemical Sciences and Technology (CNR - SCITEC), via Mario Bianco 9, 20131, Milan, Italy.
| | - L Sola
- National Research Council of Italy - Institute of Chemical Sciences and Technology (CNR - SCITEC), via Mario Bianco 9, 20131, Milan, Italy
| | - F Damin
- National Research Council of Italy - Institute of Chemical Sciences and Technology (CNR - SCITEC), via Mario Bianco 9, 20131, Milan, Italy
| | - A Mussida
- National Research Council of Italy - Institute of Chemical Sciences and Technology (CNR - SCITEC), via Mario Bianco 9, 20131, Milan, Italy
| | - M Chiari
- National Research Council of Italy - Institute of Chemical Sciences and Technology (CNR - SCITEC), via Mario Bianco 9, 20131, Milan, Italy
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Bolognesi M, Prosa M, Toerker M, Lopez Sanchez L, Wieczorek M, Giacomelli C, Benvenuti E, Pellacani P, Elferink A, Morschhauser A, Sola L, Damin F, Chiari M, Whatton M, Haenni E, Kallweit D, Marabelli F, Peters J, Toffanin S. A Fully Integrated Miniaturized Optical Biosensor for Fast and Multiplexing Plasmonic Detection of High- and Low-Molecular-Weight Analytes. Adv Mater 2023:e2208719. [PMID: 36932736 DOI: 10.1002/adma.202208719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Optical biosensors based on plasmonic sensing schemes combine high sensitivity and selectivity with label-free detection. However, the use of bulky optical components is still hampering the possibility of obtaining miniaturized systems required for analysis in real settings. Here, a fully miniaturized optical biosensor prototype based on plasmonic detection is demonstrated, which enables fast and multiplex sensing of analytes with high- and low molecular weight (80 000 and 582 Da) as quality and safety parameters for milk: a protein (lactoferrin) and an antibiotic (streptomycin). The optical sensor is based on the smart integration of: i) miniaturized organic optoelectronic devices used as light-emitting and light-sensing elements and ii) a functionalized nanostructured plasmonic grating for highly sensitive and specific localized surface plasmon resonance (SPR) detection. The sensor provides quantitative and linear response reaching a limit of detection of 10-4 refractive index units once it is calibrated by standard solutions. Analyte-specific and rapid (15 min long) immunoassay-based detection is demonstrated for both targets. By using a custom algorithm based on principal-component analysis, a linear dose-response curve is constructed which correlates with a limit of detection (LOD) as low as 3.7 µg mL-1 for lactoferrin, thus assessing that the miniaturized optical biosensor is well-aligned with the chosen reference benchtop SPR method.
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Affiliation(s)
- Margherita Bolognesi
- Institute of Nanostructured Materials (ISMN) - National Research Council (CNR), Via P. Gobetti 101, Bologna, 40129, Italy
| | - Mario Prosa
- Institute of Nanostructured Materials (ISMN) - National Research Council (CNR), Via P. Gobetti 101, Bologna, 40129, Italy
| | - Michael Toerker
- Fraunhofer FEP, Winterbergstraße 28, 01277, Dresden, Germany
| | | | | | | | - Emilia Benvenuti
- Institute of Nanostructured Materials (ISMN) - National Research Council (CNR), Via P. Gobetti 101, Bologna, 40129, Italy
| | - Paola Pellacani
- Plasmore s.r.l, Viale Vittorio Emanuele II 4, Pavia, 27100, Italy
| | - Alexander Elferink
- Wageningen Food Safety Research - Wageningen University and Research, Akkermaalsbos 2, Wageningen, 6708 WB, The Netherlands
| | | | - Laura Sola
- SCITEC Istituto di Scienze e Tecnologie Chimiche "G. Natta" - National Research Council (CNR), Via Mario Bianco 9, Milano, 20131, Italy
| | - Francesco Damin
- SCITEC Istituto di Scienze e Tecnologie Chimiche "G. Natta" - National Research Council (CNR), Via Mario Bianco 9, Milano, 20131, Italy
| | - Marcella Chiari
- SCITEC Istituto di Scienze e Tecnologie Chimiche "G. Natta" - National Research Council (CNR), Via Mario Bianco 9, Milano, 20131, Italy
| | - Mark Whatton
- QuadraChem Laboratories Ltd (QCL), Riverside - Forest Row Business Park, East Sussex, RH18 5DW, UK
| | - Etienne Haenni
- CSEM Center Muttenz, Tramstrasse 99, Muttenz, CH-4132, Switzerland
| | - David Kallweit
- CSEM Center Muttenz, Tramstrasse 99, Muttenz, CH-4132, Switzerland
| | - Franco Marabelli
- Physics Department - University of Pavia, Via A. Bassi 6, Pavia, 27100, Italy
| | - Jeroen Peters
- Wageningen Food Safety Research - Wageningen University and Research, Akkermaalsbos 2, Wageningen, 6708 WB, The Netherlands
| | - Stefano Toffanin
- Institute of Nanostructured Materials (ISMN) - National Research Council (CNR), Via P. Gobetti 101, Bologna, 40129, Italy
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Damin F, Galbiati S, Clementi N, Ferrarese R, Mancini N, Sola L, Chiari M. Dual-Domain Reporter Approach for Multiplex Identification of Major SARS-CoV-2 Variants of Concern in a Microarray-Based Assay. Biosensors (Basel) 2023; 13:269. [PMID: 36832035 PMCID: PMC9953785 DOI: 10.3390/bios13020269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Since the emergence of the COVID-19 pandemic in December 2019, the SARS-CoV-2 virus continues to evolve into many variants emerging around the world. To enable regular surveillance and timely adjustments in public health interventions, it is of the utmost importance to accurately monitor and track the distribution of variants as rapidly as possible. Genome sequencing is the gold standard for monitoring the evolution of the virus, but it is not cost-effective, rapid and easily accessible. We have developed a microarray-based assay that can distinguish known viral variants present in clinical samples by simultaneously detecting mutations in the Spike protein gene. In this method, the viral nucleic acid, extracted from nasopharyngeal swabs, after RT-PCR, hybridizes in solution with specific dual-domain oligonucleotide reporters. The domains complementary to the Spike protein gene sequence encompassing the mutation form hybrids in solution that are directed by the second domain ("barcode" domain) at specific locations on coated silicon chips. The method utilizes characteristic fluorescence signatures to unequivocally differentiate, in a single assay, different known SARS-CoV-2 variants. In the nasopharyngeal swabs of patients, this multiplex system was able to genotype the variants which have caused waves of infections worldwide, reported by the WHO as being of concern (VOCs), namely Alpha, Beta, Gamma, Delta and Omicron variants.
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Affiliation(s)
- Francesco Damin
- National Research Council of Italy, Institute of Chemical Sciences and Technologies “G. Natta”, 20131 Milan, Italy
| | - Silvia Galbiati
- Complications of Diabetes Units, Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Roberto Ferrarese
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Laura Sola
- National Research Council of Italy, Institute of Chemical Sciences and Technologies “G. Natta”, 20131 Milan, Italy
| | - Marcella Chiari
- National Research Council of Italy, Institute of Chemical Sciences and Technologies “G. Natta”, 20131 Milan, Italy
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Sola L, Abdel Mallak L, Damin F, Mussida A, Brambilla D, Chiari M. Optimization of Functional Group Concentration of N, N-Dimethylacrylamide-based Polymeric Coatings and Probe Immobilization for DNA and Protein Microarray Applications. Micromachines (Basel) 2023; 14:302. [PMID: 36838001 PMCID: PMC9961972 DOI: 10.3390/mi14020302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
We report here a deep investigation into the effect of the concentration of a polymeric coating's functional groups on probe density immobilization with the aim of establishing the optimal formulation to be implemented in specific microarray applications. It is widely known that the ideal performance of a microarray strictly depends on the way probes are tethered to the surface since it influences the way they interact with the complementary target. The N, N-dimethylacrylamide-based polymeric coating introduced by our research group in 2004 has already proven to offer great flexibility for the customization of surface properties; here, we demonstrate that it also represents the perfect scaffold for the modulation of probe grafting. With this aim in mind, polymers with increasing concentrations of N-acryloyloxysuccinimide (NAS) were synthesized and the coating procedure optimized accordingly. These were then tested not only in DNA microarray assays, but also using protein probes (with different MWs) to establish which formulation improves the assay performance in specific applications. The flexibility of this polymeric platform allowed us also to investigate a different immobilization chemistry-specifically, click chemistry reactions, thanks to the insertion of azide groups into the polymer chains-and to evaluate possible differences generated by this modification.
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Sola L, Brambilla D, Mussida A, Damin F, Chiari M. A Bifunctional Polymeric Coating for the Co-Immobilization of Proteins and Peptides on Microarray Substrates. Methods Mol Biol 2023; 2578:27-39. [PMID: 36152278 DOI: 10.1007/978-1-0716-2732-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The analytical performance of the microarray technique in screening the affinity and reactivity of molecules toward a specific target is highly affected by the coupling chemistry adopted to bind probes to the surface. However, the surface functionality limits the biomolecules that can be attached to the surface to a single type of molecule, thus forcing the execution of separate analyses to compare the performance of different species in recognizing their targets. Here, we introduce a new N,N-dimethylacrylamide-based polymeric coating, bearing simultaneously different functionalities (N-acryloyloxysuccinimide and azide groups) to allow an easy and straightforward method to co-immobilize proteins and oriented peptides on the same substrate. The bifunctional copolymer has been obtained by partial post-polymerization modification of the functional groups of a common precursor. This strategy represents a convenient method to reduce the number of analyses, therefore possible systematic or random errors, besides offering a drastic shortage in time, reagents, and costs.
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Affiliation(s)
- Laura Sola
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy.
| | - Dario Brambilla
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Alessandro Mussida
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
- Dipartimento di Scienze Farmaceutiche (DISFARM), Università degli Studi di Milano, Milan, Italy
| | - Francesco Damin
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Marcella Chiari
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
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Borga P, Milesi F, Peserico N, Groppi C, Damin F, Sola L, Piedimonte P, Fincato A, Sampietro M, Chiari M, Melloni A, Bertacco R. Active Opto-Magnetic Biosensing with Silicon Microring Resonators. Sensors (Basel) 2022; 22:3292. [PMID: 35590981 PMCID: PMC9105977 DOI: 10.3390/s22093292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 02/04/2023]
Abstract
Integrated optical biosensors are gaining increasing attention for their exploitation in lab-on-chip platforms. The standard detection method is based on the measurement of the shift of some optical quantity induced by the immobilization of target molecules at the surface of an integrated optical element upon biomolecular recognition. However, this requires the acquisition of said quantity over the whole hybridization process, which can take hours, during which any external perturbation (e.g., temperature and mechanical instability) can seriously affect the measurement and contribute to a sizeable percentage of invalid tests. Here, we present a different assay concept, named Opto-Magnetic biosensing, allowing us to optically measure off-line (i.e., post hybridization) tiny variations of the effective refractive index seen by microring resonators upon immobilization of magnetic nanoparticles labelling target molecules. Bound magnetic nanoparticles are driven in oscillation by an external AC magnetic field and the corresponding modulation of the microring transfer function, due to the effective refractive index dependence on the position of the particles above the ring, is recorded using a lock-in technique. For a model system of DNA biomolecular recognition we reached a lowest detected concentration on the order of 10 pm, and data analysis shows an expected effective refractive index variation limit of detection of 7.5×10-9 RIU, in a measurement time of just a few seconds.
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Affiliation(s)
- Piero Borga
- Dipartimento di Fisica, Politecnico di Milano, Via G. Colombo 81, 20133 Milano, Italy; (F.M.); (C.G.); (R.B.)
| | - Francesca Milesi
- Dipartimento di Fisica, Politecnico di Milano, Via G. Colombo 81, 20133 Milano, Italy; (F.M.); (C.G.); (R.B.)
| | - Nicola Peserico
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio, 34/5, 20133 Milano, Italy; (N.P.); (P.P.); (M.S.); (A.M.)
| | - Chiara Groppi
- Dipartimento di Fisica, Politecnico di Milano, Via G. Colombo 81, 20133 Milano, Italy; (F.M.); (C.G.); (R.B.)
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, Via Mario Bianco 9, 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Laura Sola
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, Via Mario Bianco 9, 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Paola Piedimonte
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio, 34/5, 20133 Milano, Italy; (N.P.); (P.P.); (M.S.); (A.M.)
| | | | - Marco Sampietro
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio, 34/5, 20133 Milano, Italy; (N.P.); (P.P.); (M.S.); (A.M.)
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, Via Mario Bianco 9, 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Andrea Melloni
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio, 34/5, 20133 Milano, Italy; (N.P.); (P.P.); (M.S.); (A.M.)
| | - Riccardo Bertacco
- Dipartimento di Fisica, Politecnico di Milano, Via G. Colombo 81, 20133 Milano, Italy; (F.M.); (C.G.); (R.B.)
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Brambilla D, Mussida A, Ferretti AM, Sola L, Damin F, Chiari M. Polymeric Coating of Silica Microspheres for Biological Applications: Suppression of Non-Specific Binding and Functionalization with Biomolecules. Polymers (Basel) 2022; 14:polym14040730. [PMID: 35215642 PMCID: PMC8877092 DOI: 10.3390/polym14040730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
The use of micro- and nanoparticles in biological applications has dramatically grown during the last few decades due to the ease of protocols development and compatibility with microfluidics devices. Particles can be composed by different materials, i.e., polymers, inorganic dielectrics, and metals. Among them, silica is a suitable material for the development of biosensing applications. Depending on their final application, the surface properties of particles, including silica, are tailored by means of chemical modification or polymeric coating. The latter strategy represents a powerful tool to create a hydrophilic environment that enables the functionalization of particles with biomolecules and the further interaction with analytes. Here, the use of MCP-6, a dimethylacrylamide (DMA)-based ter-copolymer, to coat silica microspheres is presented. MCP-6 offers unprecedented ease of coating, imparting silica particles a hydrophilic coating with antifouling properties that is able to provide high-density immobilization of biological probes.
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Sola L, Brambilla D, Mussida A, Consonni R, Damin F, Cretich M, Gori A, Chiari M. A bi-functional polymeric coating for the co-immobilization of proteins and peptides on microarray substrates. Anal Chim Acta 2021; 1187:339138. [PMID: 34753566 DOI: 10.1016/j.aca.2021.339138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
The analytical performance of the microarray technique in screening the affinity and reactivity of molecules towards a specific target, is highly affected by the coupling chemistry adopted to bind probes to the surface. However, the surface functionality limits the biomolecules that can be attached to the surface to a single type of molecule, thus forcing the execution of separate analyses to compare the performance of different species in recognizing their targets. Here we introduce a new N, N-dimethylacrylamide-based polymeric coating, bearing simultaneously different functionalities (N-acryloyloxysuccinimide and azide groups) to allow an easy and straightforward method to co-immobilize proteins and oriented peptides on the same substrate. The bi-functional copolymer has been obtained by partial post polymerization modification of the functional groups of a common precursor. A NMR characterization of the copolymer was conducted to quantify the percentage of NAS that has been transformed into azido groups. The polymer was used to coat surfaces onto which both native antibodies and alkyne modified peptides were immobilized, to perform the phenotype characterization of extracellular vesicles (EVs). This strategy represents a convenient method to reduce the number of analysis, thus possible systematic or random errors, besides offering a drastic shortage in time, reagents and costs.
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Affiliation(s)
- Laura Sola
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy.
| | - Dario Brambilla
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Alessandro Mussida
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Roberto Consonni
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Marina Cretich
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Galbiati S, Damin F, Brambilla D, Ferraro L, Soriani N, Ferretti AM, Burgio V, Ronzoni M, Vago R, Sola L, Chiari M. Small EVs-Associated DNA as Complementary Biomarker to Circulating Tumor DNA in Plasma of Metastatic Colorectal Cancer Patients. Pharmaceuticals (Basel) 2021; 14:ph14020128. [PMID: 33562158 PMCID: PMC7915475 DOI: 10.3390/ph14020128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/30/2022] Open
Abstract
It is widely accepted that assessing circular tumor DNA (ctDNA) in the plasma of cancer patients is a promising practice to evaluate somatic mutations from solid tumors noninvasively. Recently, it was reported that isolation of extracellular vesicles improves the detection of mutant DNA from plasma in metastatic patients; however, no consensus on the presence of dsDNA in exosomes has been reached yet. We analyzed small extracellular vesicle (sEV)-associated DNA of eleven metastatic colorectal cancer (mCRC) patients and compared the results obtained by microarray and droplet digital PCR (ddPCR) to those reported on the ctDNA fraction. We detected the same mutations found in tissue biopsies and ctDNA in all samples but, unexpectedly, in one sample, we found a KRAS mutation that was not identified either in ctDNA or tissue biopsy. Furthermore, to assess the exact location of sEV-associated DNA (outside or inside the vesicle), we treated with DNase I sEVs isolated with three different methodologies. We found that the DNA inside the vesicles is only a small fraction of that surrounding the vesicles. Its amount seems to correlate with the total amount of circulating tumor DNA. The results obtained in our experimental setting suggest that integrating ctDNA and sEV-associated DNA in mCRC patient management could provide a complete real-time assessment of the cancer mutation status.
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Affiliation(s)
- Silvia Galbiati
- Complications of Diabetes Units, Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Correspondence: (S.G.); (F.D.)
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, 20131 Milan, Italy; (D.B.); (L.F.); (A.M.F.); (L.S.); (M.C.)
- Correspondence: (S.G.); (F.D.)
| | - Dario Brambilla
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, 20131 Milan, Italy; (D.B.); (L.F.); (A.M.F.); (L.S.); (M.C.)
| | - Lucia Ferraro
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, 20131 Milan, Italy; (D.B.); (L.F.); (A.M.F.); (L.S.); (M.C.)
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Anna M. Ferretti
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, 20131 Milan, Italy; (D.B.); (L.F.); (A.M.F.); (L.S.); (M.C.)
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, 20132 Milan, Italy; (V.B.); (M.R.)
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, 20132 Milan, Italy; (V.B.); (M.R.)
| | - Riccardo Vago
- Urological Research Institute, Division of Experimental Oncology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy;
- Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Laura Sola
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, 20131 Milan, Italy; (D.B.); (L.F.); (A.M.F.); (L.S.); (M.C.)
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” SCITEC CNR, 20131 Milan, Italy; (D.B.); (L.F.); (A.M.F.); (L.S.); (M.C.)
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12
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Galbiati S, Damin F, Ferraro L, Soriani N, Burgio V, Ronzoni M, Gianni L, Ferrari M, Chiari M. Microarray Approach Combined with ddPCR: An Useful Pipeline for the Detection and Quantification of Circulating Tumour dna Mutations. Cells 2019; 8:cells8080769. [PMID: 31344983 PMCID: PMC6721623 DOI: 10.3390/cells8080769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
It has now been established that in biological fluids such as blood, it is possible to detect cancer causing genomic alterations by analysing circulating tumour DNA (ctDNA). Information derived from ctDNA offers a unique opportunity to enrich our understanding of cancer biology, tumour evolution and therapeutic efficacy and resistance. Here, we propose a workflow to identify targeted mutations by a customized microarray-based assay for the simultaneous detection of single point mutations in different oncogenes (KRAS, NRAS and BRAF) followed by droplet digital PCR (ddPCR) to determine the fractional abundance of the mutated allele. Genetic variants were determined in the plasma of 20 metastatic colorectal cancer (mCRC) patients previously genotyped on tissue biopsy at the diagnosis for medication planning (T0) and following the tumour genetic evolution during treatment phase (T1 and T2) with the objective of allowing therapy response prediction and monitoring. Our preliminary results show that this combined approach is suitable for routine clinical practice. The microarray platform enables for a rapid, specific and sensitive detection of the most common mutations suitable for high-throughput analysis without costly instrumentation while, the ddPCR, consents an absolute quantification of the mutated allele in a longitudinal observational study on patients undergoing targeted therapy.
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Affiliation(s)
- Silvia Galbiati
- Genomic Unit for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Lucia Ferraro
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Nadia Soriani
- Genomic Unit for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Luca Gianni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Maurizio Ferrari
- Genomic Unit for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
- Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
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Sola L, Romanato A, Siboni MB, Damin F, Chiodi E, Brambilla D, Cretich M, Gori A, Chiari M. Layer-by-layer deposition of functional click polymers for microarray applications. EXPRESS POLYM LETT 2019. [DOI: 10.3144/expresspolymlett.2019.87] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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14
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Damin F, Galbiati S, Soriani N, Burgio V, Ronzoni M, Ferrari M, Chiari M. Analysis of KRAS, NRAS and BRAF mutational profile by combination of in-tube hybridization and universal tag-microarray in tumor tissue and plasma of colorectal cancer patients. PLoS One 2018; 13:e0207876. [PMID: 30562355 PMCID: PMC6298683 DOI: 10.1371/journal.pone.0207876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/06/2018] [Indexed: 01/05/2023] Open
Abstract
Microarray technology fails in detecting point mutations present in a small fraction of cells from heterogeneous tissue samples or in plasma in a background of wild-type cell-free circulating tumor DNA (ctDNA). The aim of this study is to overcome the lack of sensitivity and specificity of current microarray approaches introducing a rapid and sensitive microarray-based assay for the multiplex detection of minority mutations of oncogenes (KRAS, NRAS and BRAF) with relevant diagnostics implications in tissue biopsies and plasma samples in metastatic colorectal cancer patients. In our approach, either wild-type or mutated PCR fragments are hybridized in solution, in a temperature gradient, with a set of reporters with a 5' domain, complementary to the target sequences and a 3' domain complementary to a surface immobilized probe. Upon specific hybridization in solution, which occurs specifically thanks to the temperature gradients, wild-type and mutated samples are captured at specific location on the surface by hybridization of the 3' reporter domain with its complementary immobilized probe sequence. The most common mutations in KRAS, NRAS and BRAF genes were detected in less than 90 minutes in tissue biopsies and plasma samples of metastatic colorectal cancer patients. Moreover, the method was able to reveal mutant alleles representing less than 0,3% of total DNA. We demonstrated detection limits superior to those provided by many current technologies in the detection of RAS and BRAF gene superfamily mutations, a level of sensitivity compatible with the analysis of cell free circulating tumor DNA in liquid biopsy.
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Affiliation(s)
- Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
- * E-mail:
| | - Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
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15
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Galbiati S, Damin F, Burgio V, Brisci A, Soriani N, Belcastro B, Di Resta C, Gianni L, Chiari M, Ronzoni M, Ferrari M. Evaluation of three advanced methodologies, COLD-PCR, microarray and ddPCR, for identifying the mutational status by liquid biopsies in metastatic colorectal cancer patients. Clin Chim Acta 2018; 489:136-143. [PMID: 30550935 DOI: 10.1016/j.cca.2018.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 01/22/2023]
Abstract
A major effort has been focused on the detection of oncogenes' mutations in diverse types of clinical specimens including formalin-fixed and paraffin embedded tissues, presently the gold-standard samples, up to plasma, that constitute a noninvasive alternative source of tumor DNA. The reliable detection of mutations in circulating tumor DNA requires a high analytical sensitivity. Here, we applied three different highly sensitive methodologies (COLD-PCR, a microarray-based approach and the droplet digital PCR, ddPCR) to identify mutations in the plasma of 30 metastatic colorectal cancer patients previously genotyped on tissue biopsy. The methods showed a modest concordance rate with respect to the results obtained on tissue biopsies: 63.3% by ddPCR, 63% by microarray and 55.6% by COLD-PCR. This could be ascribed either to the different timing between tissue and liquid biopsy collection, which could reflect a different stage of disease progression or to the diverse sensitivity of the methodologies applied. Indeed, if we compare the results obtained on plasma samples, the concordance rates were higher especially by comparing ddPCR versus COLD-PCR (92.6%). Thus, we consider both methodologies as useful procedures easily transferable in a clinical setting. Notably, the ddPCR allows a quantitative assessment of the fractional abundance of the mutation.
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Affiliation(s)
- Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Francesco Damin
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Angela Brisci
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernadette Belcastro
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Di Resta
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Gianni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy; Università Vita-Salute San Raffaele, Milano, Italy
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Sola L, Gagni P, D’Annessa I, Capelli R, Bertino C, Romanato A, Damin F, Bergamaschi G, Marchisio E, Cuzzocrea A, Bombaci M, Grifantini R, Chiari M, Colombo G, Gori A, Cretich M. Enhancing Antibody Serodiagnosis Using a Controlled Peptide Coimmobilization Strategy. ACS Infect Dis 2018; 4:998-1006. [PMID: 29570266 DOI: 10.1021/acsinfecdis.8b00014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antigen immunoreactivity is often determined by surface regions defined by the 3D juxtapositions of amino acids stretches that are not continuous in the linear sequence. As such, mimicking an antigen immunoreactivity by means of putative linear peptide epitopes for diagnostic purposes is not trivial. Here we present a straightforward and robust method to extend the reach of immune-diagnostic probes design by copresenting peptides belonging to the same antigenic surface. In this case study focused on a computationally predicted Zika virus NS1 protein putative antigenic region, we reached a diagnostic confidence by the oriented and spatially controlled coimmobilization of peptide sequences found adjacent within the protein fold, that cooperatively interacted to provide enhanced immunoreactivity with respect to single linear epitopes. Through our method, we were able to differentiate Zika infected individuals from healthy controls. Remarkably, our strategy fits well with the requirements to build high-throughput screening platforms of linear and mixed peptide libraries, and it could possibly facilitate the rapid identification of conformational immunoreactive regions.
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Affiliation(s)
- Laura Sola
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Paola Gagni
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Ilda D’Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Riccardo Capelli
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Camilla Bertino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Alessandro Romanato
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Francesco Damin
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Greta Bergamaschi
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Edoardo Marchisio
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Angela Cuzzocrea
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Mauro Bombaci
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Renata Grifantini
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
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Sola L, Damin F, Gagni P, Consonni R, Chiari M. Synthesis of Clickable Coating Polymers by Postpolymerization Modification: Applications in Microarray Technology. Langmuir 2016; 32:10284-10295. [PMID: 27632284 DOI: 10.1021/acs.langmuir.6b02816] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this paper, we report on the postpolymerization modification (PPM) of a polymer to introduce new functionalities that enable click chemistry reactions for microarray applications. The parent polymer, named copoly(DMA-NAS-MAPS), is composed of N,N-dimethylacrylamide (DMA), a monomer that self-adsorbs onto different materials through weak interactions such as hydrogen bonding or van der Waals forces, 3-(trimethoxysilyl)propyl methacrylate (MAPS) that strengthens the stability of the coating through the formation of covalent bonds with siloxane groups on the surface to be coated, and N-acryloyloxysuccinimide (NAS), an active ester group, highly reactive toward nucleophiles, which enables bioprobe immobilization. This copolymer has been widely exploited to coat surfaces for microarray applications but exhibits some limitations because of the potential hydrolysis of the active ester (NHS ester). The degradation of the NHS ester hampers the use of this coating in some situations, for example, when probe immobilization cannot be accomplished through a microspotting situation, but in large volumes, for example, in microchannel derivatization or micro-/nanoparticle functionalization. To overcome the limitations of NHS esters, we have developed a family of polymers that originate from the common copolymer precursor, by reacting the active ester contained in the polymer chain with a bifunctional amine. In particular, the functional groups introduced in the polymer using PPM enable click chemistry reactions such as azide/alkyne or thiol/maleimide "click" reactions, with suitably modified biomolecules. The advantages of such reactions are quantitative yields, orthogonality of functional groups, and insensitivity of the reaction to pH. The new click functionalities, inserted with quantitative yields, improve the stability of the coating, enabling the attachment of biomolecules directly from a solution and avoiding the spotting of reduced volumes (pL) of probes. Finally, we have demonstrated the applicability of the click surfaces in a highly effective solid-phase PCR for the genotyping of the G12D KRAS mutation.
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Affiliation(s)
- Laura Sola
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milano, Italy
| | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milano, Italy
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milano, Italy
| | - Roberto Consonni
- Istituto per lo Studio delle Macromolecole, CNR , Via Corti 12, 20133 Milano, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milano, Italy
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18
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Nava G, Ceccarello E, Giavazzi F, Salina M, Damin F, Chiari M, Buscaglia M, Bellini T, Zanchetta G. Label-free detection of DNA single-base mismatches using a simple reflectance-based optical technique. Phys Chem Chem Phys 2016; 18:13395-402. [PMID: 27122358 DOI: 10.1039/c5cp08017g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid and quantitative detection of the binding of nucleic acids to surface-immobilized probes remains a challenge in many biomedical applications. We investigated the hybridization of a set of fully complementary and defected 12-base long DNA oligomers by using the Reflective Phantom Interface (RPI), a recently developed multiplexed label-free detection technique. Based on the simple measurement of reflected light intensity, this technology enables to quantify the hybridization directly as it occurs on the surface with a sensitivity of 10 pg mm(-2). We found a strong effect of single-base mismatches and of their location on hybridization kinetics and equilibrium binding. In line with previous studies, we found that DNA-DNA binding is weaker on a surface than in the bulk. Our data indicate that this effect is a consequence of weak nonspecific binding of the probes to the surface.
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Affiliation(s)
- G Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
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Castagna R, Bertucci A, Prasetyanto EA, Monticelli M, Conca DV, Massetti M, Sharma PP, Damin F, Chiari M, De Cola L, Bertacco R. Reactive Microcontact Printing of DNA Probes on (DMA-NAS-MAPS) Copolymer-Coated Substrates for Efficient Hybridization Platforms. Langmuir 2016; 32:3308-3313. [PMID: 26972953 DOI: 10.1021/acs.langmuir.5b04669] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
High-performing hybridization platforms fabricated by reactive microcontact printing of DNA probes are presented. Multishaped PDMS molds are used to covalently bind oligonucleotides over a functional copolymer (DMA-NAS-MAPS) surface. Printed structures with minimum width of about 1.5 μm, spaced by 10 μm, are demonstrated, with edge corrugation lower than 300 nm. The quantification of the immobilized surface probes via fluorescence imaging gives a remarkable concentration of 3.3 × 10(3) oligonucleotides/μm(2), almost totally active when used as probes in DNA-DNA hybridization assays. Indeed, fluorescence and atomic force microscopy show a 95% efficiency in target binding and uniform DNA hybridization over printed areas.
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Affiliation(s)
- Rossella Castagna
- Dipartimento di Elettronica Informazione e Bioingegneria, Politecnico di Milano , Via G. Colombo 81, 20133, Milano, Italy
| | - Alessandro Bertucci
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg , 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Eko Adi Prasetyanto
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg , 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Marco Monticelli
- Dipartimento di Fisica, Politecnico di Milano , Via G. Colombo 81, 20133, Milano, Italy
| | - Dario Valter Conca
- Dipartimento di Fisica, Politecnico di Milano , Via G. Colombo 81, 20133, Milano, Italy
| | - Matteo Massetti
- Dipartimento di Fisica, Politecnico di Milano , Via G. Colombo 81, 20133, Milano, Italy
| | | | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , Via Mario Bianco 9, 20131, Milano, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , Via Mario Bianco 9, 20131, Milano, Italy
| | - Luisa De Cola
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg , 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Riccardo Bertacco
- Dipartimento di Fisica, Politecnico di Milano , Via G. Colombo 81, 20133, Milano, Italy
- IFN-CNR Via Colombo 81, 20133 Milano, Italy
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Galbiati S, Monguzzi A, Damin F, Soriani N, Passiu M, Castellani C, Natacci F, Curcio C, Seia M, Lalatta F, Chiari M, Ferrari M, Cremonesi L. COLD-PCR and microarray: two independent highly sensitive approaches allowing the identification of fetal paternally inherited mutations in maternal plasma. J Med Genet 2016; 53:481-7. [PMID: 26912453 DOI: 10.1136/jmedgenet-2015-103229] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 02/03/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Until now, non-invasive prenatal diagnosis of genetic diseases found only limited routine applications. In autosomal recessive diseases, it can be used to determine the carrier status of the fetus through the detection of a paternally inherited disease allele in cases where maternal and paternal mutated alleles differ. METHODS Conditions for non-invasive identification of fetal paternally inherited mutations in maternal plasma were developed by two independent approaches: coamplification at lower denaturation temperature-PCR (COLD-PCR) and highly sensitive microarrays. Assays were designed for identifying 14 mutations, 7 causing β-thalassaemia and 7 cystic fibrosis. RESULTS In total, 87 non-invasive prenatal diagnoses were performed by COLD-PCR in 75 couples at risk for β-thalassaemia and 12 for cystic fibrosis. First, to identify the more appropriate methodology for the analysis of minority mutated fetal alleles in maternal plasma, both fast and full COLD-PCR protocols were developed for the most common Italian β-thalassaemia Cd39 and IVSI.110 mutations. In 5 out of 31 samples, no enrichment was obtained with the fast protocol, while full COLD-PCR provided the correct fetal genotypes. Thus, full COLD-PCR protocols were developed for all the remaining mutations and all analyses confirmed the fetal genotypes obtained by invasive prenatal diagnosis. Microarray analysis was performed on 40 samples from 28 couples at risk for β-thalassaemia and 12 for cystic fibrosis. Results were in complete concordance with those obtained by both COLD-PCR and invasive procedures. CONCLUSIONS COLD-PCR and microarray approaches are not expensive, simple to handle, fast and can be easily set up in specialised clinical laboratories where prenatal diagnosis is routinely performed.
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Affiliation(s)
- Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Monguzzi
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marianna Passiu
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Carlo Castellani
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Federica Natacci
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Curcio
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Seia
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Faustina Lalatta
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy Università Vita-Salute San Raffaele, Milano, Italy
| | - Laura Cremonesi
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Damin F, Galbiati S, Ferrari M, Chiari M. DNA microarray-based solid-phase PCR on copoly (DMA-NAS-MAPS) silicon coated slides: An example of relevant clinical application. Biosens Bioelectron 2015; 78:367-373. [PMID: 26655175 DOI: 10.1016/j.bios.2015.11.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
In a previous study we developed a highly sensitive DNA microarray for the detection of common KRAS oncogenic mutations, which has been proven to be highly specific in assigning the correct genotype without any enrichment strategy even in the presence of minority mutated alleles. However, in this approach, the need of a spotter for the deposition of the purified PCR products on the substrates and the purification step of the conventional PCR are serious drawbacks. To overcome these limitations we have introduced the solid-phase polymerase chain reaction (SP-PCR) to form the array of PCR products starting from the oligonucleotide primers. This work was possible thanks to the great thermal stability of the copoly (DMA-NAS-MAPS) coating which withstands PCR thermal cycling temperatures. As an example of the application of this platform we performed the analysis of six common mutations in the codon 12 of KRAS gene (G12A, G12C, G12D, G12R, G12S, and G12V). In conclusion solid-phase PCR, combined with dual-color hybridization, allows mutation analysis in a shorter time span and is more suitable for automation.
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Affiliation(s)
- Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy.
| | - Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy
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Zilio C, Sola L, Damin F, Faggioni L, Chiari M. Erratum to: Universal hydrophilic coating of thermoplastic polymers currently used in microfluidics. Biomed Microdevices 2014. [DOI: 10.1007/s10544-014-9840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Platt GW, Damin F, Swann MJ, Metton I, Skorski G, Cretich M, Chiari M. Allergen immobilisation and signal amplification by quantum dots for use in a biosensor assay of IgE in serum. Biosens Bioelectron 2014; 52:82-8. [DOI: 10.1016/j.bios.2013.08.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 12/01/2022]
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Albisetti E, Petti D, Cantoni M, Damin F, Torti A, Chiari M, Bertacco R. Conditions for efficient on-chip magnetic bead detection via magnetoresistive sensors. Biosens Bioelectron 2013; 47:213-7. [DOI: 10.1016/j.bios.2013.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 11/26/2022]
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Galbiati S, Monguzzi A, Soriani N, Stenirri S, Lalatta F, Seia M, Restagno G, Damin F, Chiari M, Ferrari M. Non-invasive prenatal diagnosis of genetic diseases by advanced technologies. Clin Biochem 2013. [DOI: 10.1016/j.clinbiochem.2013.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Giavazzi F, Salina M, Cerbino R, Bassi M, Prosperi D, Ceccarello E, Damin F, Sola L, Rusnati M, Chiari M, Chini B, Bellini T, Buscaglia M. Multispot, label-free biodetection at a phantom plastic-water interface. Proc Natl Acad Sci U S A 2013; 110:9350-5. [PMID: 23696673 PMCID: PMC3677498 DOI: 10.1073/pnas.1214589110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recognizing and quantifying specific biomolecules in aqueous samples are constantly needed in research and diagnostic laboratories. As the typical detection procedures are rather lengthy and involve the use of labeled secondary antibodies or other agents to provide a signal, efforts have been made over the last 10 y to develop alternative label-free methods that enable direct detection. We propose and demonstrate an extremely simple, low-cost, label-free biodetector based on measuring the intensity of light reflected by the interface between a fluid sample and an amorphous fluoropolymer substrate having a refractive index very close to that of water and hosting various antibodies immobilized in spots. Under these index-matching conditions, the amount of light reflected by the interface allows straightforward quantification of the amount of antigen binding to each spot. Using antibodies targeting heterologous immunoglobulins and antigens commonly used as markers for diagnoses of hepatitis B and HIV, we demonstrate the limit of detection of a few picograms per square millimeter of surface-bound molecules. We also show that direct and real-time access to the amount of binding molecules allows the precise extrapolation of adhesion rates, from which the concentrations of antigens in solution can be estimated down to fractions of nanograms per milliliter.
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Affiliation(s)
- Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
- Proxentia S.r.l., 20135 Milan, Italy
| | - Matteo Salina
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
- Proxentia S.r.l., 20135 Milan, Italy
| | - Roberto Cerbino
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
| | - Mattia Bassi
- Materials Science Department, Solvay Specialty Polymers Research and Development Center, 20021 Bollate, Italy
| | - Davide Prosperi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milan, Italy
| | - Erica Ceccarello
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
- Proxentia S.r.l., 20135 Milan, Italy
| | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare–Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Laura Sola
- Istituto di Chimica del Riconoscimento Molecolare–Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Marco Rusnati
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, 25123 Brescia, Italy; and
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare–Consiglio Nazionale delle Ricerche, 20131 Milan, Italy
| | - Bice Chini
- Istituto di Neuroscienze–Consiglio Nazionale delle Ricerche, 20129 Milan, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20090 Segrate, Italy
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Galbiati S, Damin F, Pinzani P, Mancini I, Vinci S, Chiari M, Orlando C, Cremonesi L, Ferrari M. A new microarray substrate for ultra-sensitive genotyping of KRAS and BRAF gene variants in colorectal cancer. PLoS One 2013; 8:e59939. [PMID: 23536897 PMCID: PMC3607556 DOI: 10.1371/journal.pone.0059939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 02/21/2013] [Indexed: 12/11/2022] Open
Abstract
Molecular diagnostics of human cancers may increase accuracy in prognosis, facilitate the selection of the optimal therapeutic regimen, improve patient outcome, reduce costs of treatment and favour development of personalized approaches to patient care. Moreover sensitivity and specificity are fundamental characteristics of any diagnostic method. We developed a highly sensitive microarray for the detection of common KRAS and BRAF oncogenic mutations. In colorectal cancer, KRAS and BRAF mutations have been shown to identify a cluster of patients that does not respond to anti-EGFR therapies; the identification of these mutations is therefore clinically extremely important. To verify the technical characteristics of the microarray system for the correct identification of the KRAS mutational status at the two hotspot codons 12 and 13 and of the BRAFV600E mutation in colorectal tumor, we selected 75 samples previously characterized by conventional and CO-amplification at Lower Denaturation temperature-PCR (COLD-PCR) followed by High Resolution Melting analysis and direct sequencing. Among these samples, 60 were collected during surgery and immediately steeped in RNAlater while the 15 remainders were formalin-fixed and paraffin-embedded (FFPE) tissues. The detection limit of the proposed method was different for the 7 KRAS mutations tested and for the V600E BRAF mutation. In particular, the microarray system has been able to detect a minimum of about 0.01% of mutated alleles in a background of wild-type DNA. A blind validation displayed complete concordance of results. The excellent agreement of the results showed that the new microarray substrate is highly specific in assigning the correct genotype without any enrichment strategy.
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Affiliation(s)
- Silvia Galbiati
- San Raffaele Scientific Institute, Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, Milan, Italy.
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Abstract
Polymeric coatings, usually referred as tridimensional chemistries, provide homogenous surface derivatization methods presenting a high reactive group concentration and resulting in an increased binding capacity of targets. Furthermore, they act as linkers distributing the bound probe also in the axial position, thus causing a faster reaction with the target involved in biomolecular recognition and can be engineered to custom tailor their properties for specific applications. Most approaches which aim at attaching polymers to a surface use a system where the polymer carries an "anchor" group either as an end group or in a side chain. This anchor group can reacts with appropriate sites at the substrate surface, thus yielding surface-attached monolayers of polymer molecules (termed "grafting to"). Another technique is to carry out a polymerization reaction in the presence of a substrate onto which monomers had been attached leading to the so called "grafting from" approach. In this chapter, protocols to functionalize glass and silicon surfaces by "grafting to" as well as by "grafting-from" approach are shown using copolymers made of N,N-dimethylacrylamide (DMA) or Glycidyl methacrylate (GMA) as the polymer backbone, N-acryloyloxysuccinimide (NAS) as reactive group, and 3-(trimethoxysilyl)propyl methacrylate (MAPS) or 3-mercaptopropyl trimethoxy silane (MPS) as anchoring groups.
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Affiliation(s)
- Laura Sola
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milan, Italy
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Brisci A, Damin F, Pietra D, Galbiati S, Boggi S, Casetti I, Rumi E, Chiari M, Cazzola M, Ferrari M, Cremonesi L. COLD-PCR and innovative microarray substrates for detecting and genotyping MPL exon 10 W515 substitutions. Clin Chem 2012; 58:1692-702. [PMID: 23065476 DOI: 10.1373/clinchem.2012.192708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Myeloproliferative neoplasms (MPNs) include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Somatic mutations in exon 10 of the MPL (myeloproliferative leukemia virus oncogene) gene, mainly substitutions encoding W515 variants, have recently been described in a minority of patients with ET or PMF. We optimized analytically sensitive methods for detecting and genotyping MPL variants. METHODS We used DNA previously isolated from circulating granulocytes of 60 patients with MPN that had previously been analyzed by high-resolution melting (HRM), direct sequencing, and the TaqMan allelic-discrimination assay. We developed conditions for enriching tumor mutant alleles with COLD-PCR (coamplification at lower denaturation temperature PCR) and coupled it with direct sequencing. Assays were designed for identifying MPL W515 substitutions with full COLD-PCR protocols. In parallel, we used innovative microarray substrates to develop assays for evaluating the mutant burden in granulocyte cells. RESULTS Mutations that were present at very low levels in patients who had previously been scored as having an MPL variant by HRM and as wild type by direct sequencing were successfully identified in granulocyte DNA. Notably, the microarray approach displayed analytical sensitivities of 0.1% to 5% mutant allele, depending on the particular mutation. This analytical sensitivity is similar to that obtained with COLD-PCR. The assay requires no enrichment strategy and allows both the characterization of each variant allele and the evaluation of its proportion in every patient. CONCLUSIONS These procedures, which are transferable to clinical diagnostic laboratories, can be used for detecting very low proportions of minority mutant alleles that cannot be identified by other, conventional methods.
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Affiliation(s)
- Angela Brisci
- San Raffaele Scientific Institute, Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, Milan, Italy.
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Cretich M, Monroe MR, Reddington A, Zhang X, Daaboul GG, Damin F, Sola L, Unlu MS, Chiari M. Interferometric silicon biochips for label and label-free DNA and protein microarrays. Proteomics 2012; 12:2963-77. [PMID: 22930463 DOI: 10.1002/pmic.201200202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/12/2022]
Abstract
Protein and DNA microarrays hold the promise to revolutionize the field of molecular diagnostics. Traditional microarray applications employ labeled detection strategies based on the use of fluorescent and chemiluminescent secondary antibodies. However, the development of high throughput, sensitive, label-free detection techniques is attracting attention as they do not require labeled reactants and provide quantitative information on binding kinetics. In this article, we will provide an overview of the recent author's work in label and label-free sensing platforms employing silicon/silicon oxide (Si/SiO(2)) substrates for interferometric and/or fluorescence detection of microarrays. The review will focus on applications of Si/SiO(2) with controlled oxide layers to (i) enhance the fluorescence intensity by optical interferences, (ii) quantify with sub-nanometer accuracy the axial locations of fluorophore-labeled probes tethered to the surface, and (iii) detect protein-protein interactions label free. Different methods of biofunctionalization of the sensing surface will be discussed. In particular, organosilanization reactions for monodimensional coatings and polymeric coatings will be extensively reviewed. Finally, the importance of calibration of protein microarrays through the dual use of labeled and label-free detection schemes on the same chip will be illustrated.
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Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
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Galbiati S, Brisci A, Damin F, Gentilin B, Curcio C, Restagno G, Cremonesi L, Ferrari M. Fetal DNA in maternal plasma: a noninvasive tool for prenatal diagnosis of beta-thalassemia. Expert Opin Biol Ther 2012; 12 Suppl 1:S181-7. [DOI: 10.1517/14712598.2012.677428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Cretich M, Bagnati M, Damin F, Sola L, Chiari M. Overcoming mass transport limitations to achieve femtomolar detection limits on silicon protein microarrays. Anal Biochem 2011; 418:164-6. [DOI: 10.1016/j.ab.2011.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/04/2011] [Accepted: 07/05/2011] [Indexed: 10/18/2022]
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Cretich M, Damin F, Longhi R, Gotti C, Galati C, Renna L, Chiari M. Peptide microarrays on coated silicon slides for highly sensitive antibody detection. Methods Mol Biol 2010; 669:147-60. [PMID: 20857364 DOI: 10.1007/978-1-60761-845-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptides, with their well-established chemistry and fully automated synthesis, provide an invaluable tool for the screening of protein ligands, for epitope mapping, and for antibody diagnostics on the microarray format.The method described in this chapter shows that the sensitivity of a peptide-based microimmunoassay is greatly improved by using a new, specifically developed substrate made of silicon coated by an optimized layer of silicon oxide. A set of six peptides corresponding to the sequences of human and rat acetylcholine receptor subunits was immobilized on glass and silicon slides coated by a copolymer of N,N-dimethylacrylamide, N-acryloyloxysuccinimide, and 3-(trimethoxysilyl) propyl methacrylate, copoly(DMA-NAS-MAPS). The spotted probes were incubated with rabbit anti-sera and with purified antibodies raised against the corresponding peptides. The coated silicon slides, in comparison against the glass substrates, showed a five- to tenfold enhancement of the fluorescence signals, leading to the specific detection of the full set of antibodies down to a concentration of 0.5-1 ng/mL in serum. The sensitivity provided by the test allows its use for the diagnosis of antibodies in clinical samples.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare C.N.R, Milano, Italy
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Bruno F, Damin F, Causarano V, Galbiati S, Di Carlo G, Seia M, Porcaro L, Ferrari M, Chiari M, Cremonesi L. High-sensitive microarray substrates specifically designed to improve sensitivity for the identification of fetal paternally inherited sequences in maternal plasma. Clin Chem Lab Med 2009; 47:818-23. [PMID: 19496735 DOI: 10.1515/cclm.2009.187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The identification of very low-levels of minority sequences has interesting clinical and diagnostic applications. Among these, non-invasive prenatal diagnosis of genetic diseases on fetal DNA circulating in maternal plasma is an emerging field of application. METHODS A combined approach based on innovative microarray slides coated with a special copolymer was developed for the identification of three polymorphisms located in the causative gene for cystic fibrosis (CF). This technique was applied to the analysis of fetal DNA in maternal plasma from four couples that carried different allelic variants. RESULTS The use of highly sensitive slides correctly identified fetal paternally inherited alleles without any enrichment strategy. CONCLUSIONS Our results confirm that the high fluorescence signal provided by the optimized substrate may be applied to the identification of any fetal paternally inherited sequence. This helps extend the application of non-invasive prenatal diagnosis to genetic diseases caused by predominant mutations or minor rare molecular defects.
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Affiliation(s)
- Francesca Bruno
- Genomic Unit for the Diagnosis of Human Pathologies, Center for Genomics, Bioinformatics and Biostatistics, San Raffaele Scientific Institute, Milan, Italy
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Galeotti F, Chiusa I, Morello L, Gianì S, Breviario D, Hatz S, Damin F, Chiari M, Bolognesi A. Breath figures-mediated microprinting allows for versatile applications in molecular biology. Eur Polym J 2009. [DOI: 10.1016/j.eurpolymj.2009.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Oliviero G, Bergese P, Canavese G, Chiari M, Colombi P, Cretich M, Damin F, Fiorilli S, Marasso SL, Ricciardi C, Rivolo P, Depero LE. Corrigendum to “A biofunctional polymeric coating for microcantilever molecular recognition” [Anal. Chim. Acta 630 (2008) 161–167]. Anal Chim Acta 2009. [DOI: 10.1016/j.aca.2009.10.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cretich M, Sedini V, Damin F, Pelliccia M, Sola L, Chiari M. Coating of nitrocellulose for colorimetric DNA microarrays. Anal Biochem 2009; 397:84-8. [PMID: 19800859 DOI: 10.1016/j.ab.2009.09.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 09/28/2009] [Accepted: 09/29/2009] [Indexed: 11/15/2022]
Abstract
We report on the modification of a nitrocellulose film with copoly(DMA-NAS-MAPS), a tercopolymer based on N,N-dimethylacrylamide (DMA), N-acryloyloxysuccinimide (NAS), and 3-(trimethoxysilyl)propyl-methacrylate (MAPS). The chains of this polymer, interacting with nitrocellulose fibers, introduce active ester functionalities that promote the covalent binding of short oligonucleotide fragments to the nitrocellulose thin film. Using colorimetric detection, naked eye visible DNA microarrays are developed for easy identification of foodborne pathogens. The fast and robust procedure of nitrocellulose functionalization opens the opportunity to implement this material in disposable analytical microdevices that do not require sophisticated readout systems.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131 Milano, Italy.
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Galbiati S, Damin F, Di Carlo G, Ferrari M, Cremonesi L, Chiari M. Development of new substrates for high-sensitive genotyping of minority mutated alleles. Electrophoresis 2009; 29:4714-22. [PMID: 19053069 DOI: 10.1002/elps.200800242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An unsurpassed level of sensitivity was reached in the detection of minority mutated alleles. A low-density microarray was printed on a substrate specifically designed to provide an interference effect which amplifies the collection of the light emitted on the support and reinforces the intensity of excitation light. Optimal performance of the array was obtained by maximizing the probe density and the binding efficiency to the target through a polymeric coating made by the adsorption of a copolymer of N,N-dimethylacrylamide (97% of moles), N,N-acryloyloxysuccinimide (2%) and 3-(trimethoxysilyl)propyl methacrylate (1%) synthesized by free radical copolymerization. The new substrate was used in the identification of fetal mutations in the maternal plasma DNA. Amino-modified amplicons from genomic DNA corresponding to the locus of eight beta-thalassemia mutations were immobilized and interrogated with dual-color oligonucleotide targets. Compared with the conventional glass substrates, the new substrate showed a great enhancement of fluorescence signals thanks to the combination of the optics with the highly efficient polymeric coating, allowing specific detection of all mutations. The high sensitivity and selectivity obtained made it possible to develop assays for the identification of paternally inherited mutations on fetal DNA in the maternal plasma in couples at risk for beta-thalassemia.
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Affiliation(s)
- Silvia Galbiati
- Genomic Unit for the Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milan, Italy
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Yalçin A, Damin F, Ozkumur E, di Carlo G, Goldberg BB, Chiari M, Unlü MS. Direct observation of conformation of a polymeric coating with implications in microarray applications. Anal Chem 2009; 81:625-30. [PMID: 19061409 PMCID: PMC2644728 DOI: 10.1021/ac801954x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformation of a three-dimensional polymeric coating (copoly(DMA-NAS-MAPS)) and immobilization and hybridization of DNA strands on the polymer coated surface are investigated. A conformational change, specifically the swelling of the surface adsorbed polymer upon hydration, is quantified in conjunction with the application of this polymer coating for DNA microarray applications. Fluorescently labeled short DNA strands (23mers) covalently linked to the functional groups on the adsorbed polymer are used as probes to measure the swelling of the polymer. A fluorescence microscopy technique, Spectral Self-Interference Fluorescence Microscopy (SSFM), is utilized to directly measure the change in axial position of fluorophores due to swelling with subnanometer accuracy. Additionally, immobilization characteristics of single stranded DNA (ssDNA) and double stranded DNA (dsDNA) probes, as well as hybridization of ssDNA with target strands have been studied. The results show that ssDNA further away from the surface is hybridized more efficiently, which strengthens the earlier analysis of this polymeric coating as a simple but highly efficient and robust DNA microarray surface chemistry.
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Affiliation(s)
- Ayça Yalçin
- Electrical and Computer Engineering Department and Physics Department, Boston University, Boston, Massachusetts 02215, USA
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Battistella S, Damin F, Chiari M, Delgrosso K, Surrey S, Fortina P, Ferrari M, Cremonesi L. Genotyping beta-globin gene mutations on copolymer-coated glass slides with the ligation detection reaction. Clin Chem 2008; 54:1657-63. [PMID: 18703765 DOI: 10.1373/clinchem.2008.107870] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Methods are needed to analyze small amounts of samples for variation in disease-causing genes. One means is to couple the sensitivity and multiplexing capability of the ligation detection reaction (LDR) with the use of simple glass slides specifically functionalized with a novel polymer coating to enhance sensitivity. METHODS We developed an array-based genotyping assay based on glass slides coated with copolymer (N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and 3-(trimethoxysilyl)propyl methacrylate). The assay consists of an LDR with genomic DNA followed by a universal PCR (U-PCR) of genomic DNA-templated LDR product. The LDR occurs in the presence of 3 primers for each sequence variant under investigation: 2 distinguishing primers (allele specific and perfectly complementary to wild-type and mutant alleles) and 1 common locus-specific primer. The 2 allele-specific primers have different capture sequences for binding different complementary probes on a tag array. The LDR product templated from genomic DNA is made fluorescent during the U-PCR via incorporation of a Cy5-labeled universal primer into all LDR products; detection occurs on the coated glass slides. RESULTS The assay was designed to detect 7 prevalent mutations in the beta-globin gene (HBB, hemoglobin, beta) in a multiplex format, and signals for the different alleles are detected by their fluorescence. The assay was applied to 40 genomic DNA samples from both control individuals and patients with known beta-thalassemia mutations. Results show good correspondence between the patients' genotypes as assessed by DNA sequence analysis and those generated from the LDR assays. CONCLUSIONS The developed technology allows accurate identification of sequence variants in a simple, cost-effective way and offers good flexibility for scaling to other applications with different numbers of single-nucleotide polymorphisms or mutations to be detected.
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Affiliation(s)
- Stefania Battistella
- Genomic Unit for the Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano, Italy
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Chiari M, Cretich M, Damin F, Di Carlo G, Oldani C. Advanced polymers for molecular recognition and sensing at the interface. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:89-103. [DOI: 10.1016/j.jchromb.2008.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/07/2007] [Accepted: 01/04/2008] [Indexed: 11/29/2022]
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Viganò M, Levi M, Chiari M, Damin F, Turri S. Novel blocked functionality copolymers as surface coatings in DNA microarray technology. e-Polymers 2007. [DOI: 10.1515/epoly.2007.7.1.1163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractNew copolymers made of 2-(dimethyl amino) ethyl methacrylate (DMAEM) and isocyanate ethyl methacrylate blocked with methyl ethyl ketoxime (IEMB) was synthesized in various composition ratios in order to obtain water reducible copolymers after acidification. They were characterized by infrared spectroscopy, chemical titration for the determination of amine equivalent weight, and by differential scanning calorimetry (DSC). Calorimetric analysis showed the presence of a former broad endothermal peak followed by a latter, stronger exothermal one, which can be respectively attributed to the deblocking of isocyanate groups and to their subsequent reactions. Some copolymer compositions were dip coated onto microscope glass slides and surfaces were characterized by static and dynamic contact angles, revealing a clear effect of the salifying agent and a likely surface rearrangement of polar groups while in contact with water. Finally, oligonucleotides surface immobilization and molecular recognition capability of the coated glass slides were positively assessed by hybridization tests with fluorescently labelled complementary probes.
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Affiliation(s)
- M. Viganò
- 1Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - M. Levi
- 1Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - M. Chiari
- 2Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Bianco, 20100 Milan, Italy
| | - F. Damin
- 2Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Bianco, 20100 Milan, Italy
| | - S. Turri
- 1Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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Viganò M, Levi M, Turri S, Chiari M, Damin F. New copolymers of N,N-dimethylacrylamide with blocked isocyanates for oligonucleotide immobilization in DNA microarray technology. POLYMER 2007. [DOI: 10.1016/j.polymer.2007.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pirri G, Chiari M, Damin F, Meo A. Microarray glass slides coated with block copolymer brushes obtained by reversible addition chain-transfer polymerization. Anal Chem 2007; 78:3118-24. [PMID: 16643002 DOI: 10.1021/ac0521091] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reversible addition-fragmentation chain-transfer polymerization was used to prepare microarray slides grafted with polymer brushes for DNA-based applications. Block copolymer brushes of N,N-dimethylacrylamide (DMA) and glycidyl methacrylate (GMA), poly(DMA-b-GMA) were prepared by extending living poly(dimethylacrylamide) chains. The functional surface was used as a substrate for oligonucleotide hybridization experiments. The results were compared to those provided by glass slides coated by a self-assembled monolayer made of (3-glycidyloxypropyl)trimethoxysilane. Surfaces coated with block polymer brushes bearing oxirane groups are more efficient as substrates for oligonucleotide hybridization than surfaces coated with nonpolymeric self-assembled monolayers containing the same functional group. The high probe grafting density and hybridization efficiency achieved with this polymeric coating reveal the importance of the block architecture to ensure good accessibility of the immobilized probe. The new surface was characterized by static angle measurements and diffuse reflectance FT-IR spectroscopy on a silica model system.
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Affiliation(s)
- Giovanna Pirri
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy.
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Galbiati S, Restagno G, Foglieni B, Bonalumi S, Travi M, Piga A, Sbaiz L, Chiari M, Damin F, Smid M, Valsecchi L, Pasi F, Ferrari A, Ferrari M, Cremonesi L. Different approaches for noninvasive prenatal diagnosis of genetic diseases based on PNA-mediated enriched PCR. Ann N Y Acad Sci 2007; 1075:137-43. [PMID: 17108203 DOI: 10.1196/annals.1368.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aim of this work was to develop advanced and accessible protocols for noninvasive prenatal diagnosis of genetic diseases. We are evaluating different technologies for mutation detection, based on fluorescent probe hybridization of the amplified product and pyrosequencing, a technique that relies on the incorporation of nucleotides in a primer-directed polymerase extension reaction. In a previous investigation, we have already proven that these approaches are sufficiently sensitive to detect a few copies of a minority-mutated allele in the presence of an excess of wild-type DNA, In this work, in order to further enhance the sensitivity, we have employed a mutant enrichment amplification strategy based on the use of peptide nucleic acids (PNAs). These DNA analogues bind wild-type DNA, thus interfering with its amplification while still allowing the mutant DNA to become detectable. We have synthesized different PNAs, which are highly effective in clamping wild-type DNA in the beta-globin gene region, where four beta-thalassemia mutations are located (IVSI.110, CD39, IVSI.1, IVSI.6) plus HbS. The fluorescence microchip readout allows us to monitor the extent of wild-type allele inhibition, thus facilitating the assessment of the optimal PNA concentration.
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Affiliation(s)
- Silvia Galbiati
- Genomic Unit for the Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
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Suriano R, Levi M, Pirri G, Damin F, Chiari M, Turri S. Surface Behavior and Molecular Recognition in DNA Microarrays fromN,N-Dimethylacrylamide Terpolymers with Activated Esters as Linking Groups. Macromol Biosci 2006; 6:719-29. [PMID: 16967476 DOI: 10.1002/mabi.200600088] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A series of terpolymers made of DMA, NAS and MAPS were synthesized by free radical copolymerization and used as functional coatings for the fabrication of glass slide DNA microarrays. The surface properties of coated glass slides were investigated through contact angle measurements, ellipsometry and atomic force microscopy. The terpolymer molecular weight showed a moderate effect on surface tension (gamma(s) = 56-62 mN x m(-1)), but no clear effect on polymeric layer thickness (5-8 nm) and roughness. Hybridization experiments with amine-functionalized oligonucleotides gave the best fluorescence intensity results for microarrays coated with intermediate-molecular-weight terpolymers. Finally, an accelerated ageing test of the microarray in a humidity chamber showed a nice relationship between decay curves of contact angle against water and fluorescence intensity.
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Affiliation(s)
- Raffaella Suriano
- Dipartimento di Chimica, Materiali e Ingegneria Chimica Giulio Natta, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. ACTA ACUST UNITED AC 2006; 23:77-88. [PMID: 16527536 DOI: 10.1016/j.bioeng.2006.02.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 02/01/2006] [Accepted: 02/01/2006] [Indexed: 10/24/2022]
Abstract
Microarrays of proteins and peptides make it possible the screening of thousands of binding events in a parallel and high throughput fashion; therefore they are emerging as a powerful tool for proteomics and clinical assays. The complex nature of Proteome, the wide dynamic range of protein concentration in real samples and the critical role of immobilized protein orientation must be taken into account to maximize the utility of protein microarrays. Immobilization strategy and designing of an ideal local chemical environment on the solid surface are both essential for the success of a protein microarray experiment. This review article will focus on protein and peptide arrays highlighting their technical challenges and presenting new directions by means of a set of selected recent applications.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM) - C.N.R., Via Mario Bianco, 9, 20131 Milano, Italy.
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Abstract
Microarraying peptides is a powerful proteomics technique for studying molecular recognition events. Since peptides have small molecular mass, they are not easily accessible when adsorbed onto solid supports. Moreover, peptides can lack a well-defined three-dimensional structure, and therefore a correct orientation is essential to promote the interaction with their target. In this work, we investigated the suitability as a peptide array substrate of a glass slide coated with a copolymer of N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and [3-(methacryloyl-oxy)propyl]trimethoxysilyl. This polymeric surface was used as substrate for peptides in the characterization of linear antigenic sites of human chromogranin A, a useful tissue and serum marker for neuroendocrine tumors and a precursor of many biologically active peptides. The microarray support provided sufficient accessibility of the ligand, with no need for a spacer, as the polymer chains prevent interaction of immobilized peptides with substrate. In addition, the polymeric surface constitutes an aqueous micro-environment in which linear epitopes are freely exposed despite peptide random orientation. The results reported in this article are in accordance with those obtained in conventional ELISA assays using biotinylated and non-biotinylated peptides.
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Affiliation(s)
- Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Milan, Italy
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50
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Abstract
Despite the increasing interest in arraying proteins in a high-density format, several technical issues still impede the development of protein microarray technology. One of the major problems is the availability of substrates that are able to bind native proteins with high density. In this study, we investigated the suitability of a novel surface as a support for protein microarrays. A polymeric glass coating is obtained by physical adsorption of a N,N-dimethylacrylamide (DMA), N,N-acryloyloxysuccinimide (NAS), and [3-(methacryloyl-oxy)propyl]trimethoxysilyl (MAPS) copolymer. The coating procedure provides a fast and inexpensive method of producing hydrophilic functional surfaces. The slide performance was investigated in a protein-protein interaction experiment and in the assessment of rheumatoid factor (RF) in human serum samples. The results demonstrate that the ligands immobilized on the polymeric surface maintain an active conformation and are easily accessible, providing a detection limit of 54amol/spot. Moreover, in the RF assay, after hybridization with the sera, the slides have a low background, leading to a detection limit of 900amol/spot.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), C.N.R., Via Mario Bianco 9, 20131 Milano, Italy.
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