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Nava G, Carzaniga T, Casiraghi L, Bot E, Zanchetta G, Damin F, Chiari M, Weber G, Bellini T, Mollica L, Buscaglia M. Weak-cooperative binding of a long single-stranded DNA chain on a surface. Nucleic Acids Res 2024:gkae576. [PMID: 38989620 DOI: 10.1093/nar/gkae576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/04/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.
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Affiliation(s)
- Giovanni Nava
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Thomas Carzaniga
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Luca Casiraghi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Erik Bot
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Giuliano Zanchetta
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche 'Giulio Natta', National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, 20131 Milano, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche 'Giulio Natta', National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, 20131 Milano, Italy
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Tommaso Bellini
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Luca Mollica
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Marco Buscaglia
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
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Carzaniga T, Casiraghi L, Nava G, Zanchetta G, Inzani T, Chiari M, Bollati V, Epis S, Bandi C, Lai A, Zehender G, Bellini T, Buscaglia M. Serum antibody fingerprinting of SARS-CoV-2 variants in infected and vaccinated subjects by label-free microarray biosensor. Front Immunol 2024; 15:1323406. [PMID: 38476234 PMCID: PMC10927789 DOI: 10.3389/fimmu.2024.1323406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from the plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fractions. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed a larger quantity of total Ig and a lower fraction of IgA relative to the population of convalescent unvaccinated subjects.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Inzani
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, National Research Council of Italy (SCITEC-CNR), Milano, Italy
| | - Valentina Bollati
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milano, Italy
| | - Sara Epis
- Dipartimento di Bioscienze and Pediatric Clinical Research Center (CRC) ‘Fondazione Romeo ed Enrica Invernizzi’, Università degli Studi di Milano, Milano, Italy
| | - Claudio Bandi
- Dipartimento di Bioscienze and Pediatric Clinical Research Center (CRC) ‘Fondazione Romeo ed Enrica Invernizzi’, Università degli Studi di Milano, Milano, Italy
| | - Alessia Lai
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, Milano, Italy
| | - Gianguglielmo Zehender
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, Milano, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
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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 (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300947. [PMID: 37060208 DOI: 10.1002/smll.202300947] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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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 2023; 14:302. [PMID: 36838001 PMCID: PMC9961972 DOI: 10.3390/mi14020302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Nika A, Gkioka C, Machairioti F, Bilalis P, Xu J, Gajos K, Awsiuk K, Petrou P, Chatzichristidi M. Post-Polymerization Modification of Fluoropolymers via UV Irradiation in the Presence of a Photoacid Generator. Polymers (Basel) 2023; 15:polym15030493. [PMID: 36771794 PMCID: PMC9919986 DOI: 10.3390/polym15030493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 01/20/2023] Open
Abstract
Fluorinated polymers have unique wettability and protein adsorption properties. The site-specific alteration of these properties could expand their application to different research areas. In this work, a fluorinated homopolymer and two of its copolymers with 4-vinylbenzyl glycidyl ether (VBGE) are synthesized by free radical polymerization. The produced polymers are then used to develop resist formulations by the addition of a photoacid generator. Films of these formulations are exposed to ultraviolet radiation through a binary mask and heated to create the pattern. It is found that the water contact angle values of the exposed films areas are reduced compared to those of the unexposed ones, with the exception of pentafluorophenyl methacrylate (PFMA) homopolymer film. This is attributed to the reaction of the epoxy groups creating x-links and producing hydroxyl groups and the cleavage of the pentafluorophenyl group from the ester group leading to carboxylic acid groups. Both modifications on the exposed areas are verified by FTIR spectroscopy and ToF-SIMS analysis. In addition, the biomolecules adsorption ability of the exposed area is increasing 10-15 times compared to the unexposed one for the PFMA homopolymer and the PFMA/VBGE 1:1 copolymer. Thus, the proposed polymers and patterning procedure could find application to spatially directed immobilization of biomolecules and/or cells onto a surface for both biosensing and tissue engineering purposes.
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Affiliation(s)
- Anastasia Nika
- Industrial Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771 Athens, Greece
| | - Christina Gkioka
- Industrial Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771 Athens, Greece
| | - Fotini Machairioti
- Industrial Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771 Athens, Greece
- Immunoassay/Immunosensors Lab, INRaSTES, NCSR “Demokritos”, Aghia Paraskevi, 15310 Athens, Greece
| | - Panayiotis Bilalis
- Polymer Synthesis Laboratory, KAUST Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Jiaxi Xu
- Polymer Synthesis Laboratory, KAUST Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Katarzyna Gajos
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Kamil Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Panagiota Petrou
- Immunoassay/Immunosensors Lab, INRaSTES, NCSR “Demokritos”, Aghia Paraskevi, 15310 Athens, Greece
- Correspondence: (P.P.); (M.C.); Tel.: +30-210-7274335 (M.C.)
| | - Margarita Chatzichristidi
- Industrial Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771 Athens, Greece
- Correspondence: (P.P.); (M.C.); Tel.: +30-210-7274335 (M.C.)
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