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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; 52:8661-8674. [PMID: 38989620 PMCID: PMC11347152 DOI: 10.1093/nar/gkae576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Milchev A, Binder K. How does stiffness of polymer chains affect their adsorption transition? J Chem Phys 2020; 152:064901. [DOI: 10.1063/1.5139940] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- A. Milchev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - K. Binder
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
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