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Dey S, Rivas-Barbosa R, Sciortino F, Zaccarelli E, Zijlstra P. Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective. NANOSCALE 2024; 16:4872-4879. [PMID: 38318671 DOI: 10.1039/d3nr06140j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
DNA-modified gold nanoparticles (AuNPs) play a pivotal role in bio-nanotechnology, driving advancements in bio-sensing, bio-imaging, and drug delivery. Synthetic protocols have focused on maximizing the receptor density on particles by fine-tuning chemical conditions, particularly for DNA. Despite their significance, the understanding of hybridization kinetics on functionalized AuNPs is lacking, particularly how this kinetics depends on DNA density and to what extent it varies from particle-to-particle. This study explores the molecular mechanisms of DNA hybridization on densely coated AuNPs by employing a combination of single-molecule microscopy and coarse-grained molecular dynamics simulations providing a quantification of the molecular rate constants for single particles. Our findings demonstrate that DNA receptor density and the presence of spacer strands profoundly impact association kinetics, with short spacers enhancing association rates by up to ∼15-fold. In contrast, dissociation kinetics are largely unaffected by receptor density within the studied range. Single-particle analysis directly reveals variability in hybridization kinetics, which is analyzed in terms of intra- and inter-particle heterogeneity. A coarse-grained DNA model that quantifies hybridization kinetics on densely coated surfaces further corroborates our experimental results, additionally shedding light on how transient base pairing within the DNA coating influences kinetics. This integrated approach underscores the value of single-molecule studies and simulations for understanding DNA dynamics on densely coated nanoparticle surfaces, offering guidance for designing DNA-functionalized nanoparticles in sensor applications.
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Affiliation(s)
- Swayandipta Dey
- Eindhoven University of Technology, Department of Applied Physics and Science Education, Postbus 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, The Netherlands
| | - Rodrigo Rivas-Barbosa
- Dipartmento di Fisica, Universita' di Roma "La Sapienza", Piazzale Moro 5, Roma I-00185, Italy
| | - Francesco Sciortino
- Dipartmento di Fisica, Universita' di Roma "La Sapienza", Piazzale Moro 5, Roma I-00185, Italy
| | - Emanuela Zaccarelli
- Dipartmento di Fisica, Universita' di Roma "La Sapienza", Piazzale Moro 5, Roma I-00185, Italy
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Peter Zijlstra
- Eindhoven University of Technology, Department of Applied Physics and Science Education, Postbus 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, The Netherlands
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Maekawa Y, Shibuta Y, Sakata T. Effect of double-stranded DNA on electrical double layer structure at oxide/electrolyte interface in classical molecular dynamics simulation. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Barone V, Cacelli I, De Mitri N, Licari D, Monti S, Prampolini G. Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data. Phys Chem Chem Phys 2013; 15:3736-51. [PMID: 23389748 DOI: 10.1039/c3cp44179b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
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Hannestad JK, Brune R, Czolkos I, Jesorka A, El-Sagheer AH, Brown T, Albinsson B, Orwar O. Kinetics of diffusion-mediated DNA hybridization in lipid monolayer films determined by single-molecule fluorescence spectroscopy. ACS NANO 2013; 7:308-315. [PMID: 23215045 DOI: 10.1021/nn304010p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We use single-molecule fluorescence microscopy to monitor individual hybridization reactions between membrane-anchored DNA strands, occurring in nanofluidic lipid monolayer films deposited on Teflon AF substrates. The DNA molecules are labeled with different fluorescent dyes, which make it possible to simultaneously monitor the movements of two different molecular species, thus enabling tracking of both reactants and products. We employ lattice diffusion simulations to determine reaction probabilities upon interaction. The observed hybridization rate of the 40-mer DNA was more than 2-fold higher than that of the 20-mer DNA. Since the lateral diffusion coefficient of the two different constructs is nearly identical, the effective molecule radius determines the overall kinetics. This implies that when two DNA molecules approach each other, hydrogen bonding takes place distal from the place where the DNA is anchored to the surface. Strand closure then propagates bidirectionally through a zipper-like mechanism, eventually bringing the lipid anchors together. Comparison with hybridization rates for corresponding DNA sequences in solution reveals that hybridization rates are lower for the lipid-anchored strands and that the dependence on strand length is stronger.
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Affiliation(s)
- Jonas K Hannestad
- Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96, Göteborg, Sweden
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Trani F, Barone V. Silicon Nanocrystal Functionalization: Analytic Fitting of DFTB Parameters. J Chem Theory Comput 2011; 7:713-9. [PMID: 26596303 DOI: 10.1021/ct1006086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A density functional tight binding (DFTB) scheme has been applied to functionalized silicon nanocrystals. Using an analytic functional representation of DFTB parameters, the scheme has been used to compute the adsorption energies in the organic functionalization of reconstructed Si(100) and H-terminated Si(111) surfaces of hundreds-of-atoms nanocrystals. We adopt an ONIOM(QM:QM') approach that corrects the overbinding of DFTB, obtaining nice agreement with high-level reaction energies and structural configurations.
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Affiliation(s)
- Fabio Trani
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Infn Sezione di Pisa
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Infn Sezione di Pisa
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Monti S, Cacelli I, Ferretti A, Prampolini G, Barone V. Complementary and partially complementary DNA duplexes tethered to a functionalized substrate: a molecular dynamics approach to biosensing. Phys Chem Chem Phys 2011; 13:12478-87. [DOI: 10.1039/c1cp21115c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Bonanni A, Esplandiu MJ, del Valle M. Impedimetric genosensing of DNA polymorphism correlated to cystic fibrosis: A comparison among different protocols and electrode surfaces. Biosens Bioelectron 2010; 26:1245-51. [DOI: 10.1016/j.bios.2010.06.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/19/2010] [Accepted: 06/25/2010] [Indexed: 12/28/2022]
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Kalantari R, Cantor R, Chen H, Yu G, Janata J, Josowicz M. Label-Free Voltammetric Detection Using Individually Addressable Oligonucleotide Microelectrode Arrays. Anal Chem 2010; 82:9028-33. [DOI: 10.1021/ac102002k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Roya Kalantari
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ryan Cantor
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hang Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - George Yu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jiri Janata
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mira Josowicz
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Monti S, Cacelli I, Ferretti A, Prampolini G, Barone V. Simulating DNA hybridization on an amine-functionalized silicon substrate. J Phys Chem B 2010; 114:8341-9. [PMID: 20533843 DOI: 10.1021/jp103268z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of DNA biosensors to capture oligonucleotide molecules in solution is of great importance in genetics, medical diagnostics, and drug discovery. The DNA hybridization event in which the probe, which is usually a single-stranded DNA segment covalently immobilized on a functionalized surface via a cross-linker molecule, recognizes the complementary target and forms a stable duplex structure is the basis of highly specific biorecognizing devices. The rate of hybridization depends on the solvent, length of the strands, complexity of the system, and other factors and could be considerably altered by the type of attachment and by the density of the probe on the substrates. Recent experimental investigations have shown that some probes can hybridize directly from bulk solutions. In this computational study, we provide a model for the behavior of these systems choosing cross-linker, probe, and target on the basis of experimental data. MD simulations of the single-stranded DNA fragment 5'-d(TGGC)-3' attached to an allylamine-functionalized Si(111) surface through an oxanine cross-linker in aqueous solution containing the complementary sequence, i.e. 5'-d(CGCCA)-3', are presented. A possible probe-target capture mechanism obtained using explicit solvent and state-of-the-art classical molecular dynamics simulation protocols is described. The hybridization process of the tethered DNA single strand, the intermediate structures appeared during the formation of the double helix, their internal dynamics and their behavior with respect to the substrate are characterized in detail.
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Affiliation(s)
- Susanna Monti
- Istituto per i Processi Chimico-Fisici (IPCF-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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Barone V, Cacelli I, Ferretti A, Monti S, Prampolini G. Parameterization and validation of an accurate force-field for the simulation of alkylamine functionalized silicon (111) surfaces. Phys Chem Chem Phys 2010; 12:4201-9. [DOI: 10.1039/b925041g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Monti S, Cacelli I, Ferretti A, Prampolini G, Barone V. DNA hybridization mechanism on silicon nanowires: a molecular dynamics approach. MOLECULAR BIOSYSTEMS 2010; 6:2230-40. [DOI: 10.1039/c0mb00025f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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