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Li S, Coffinier Y, Lagadec C, Cleri F, Nishiguchi K, Fujiwara A, Fujii T, Kim SH, Clément N. Redox-labelled electrochemical aptasensors with nanosupported cancer cells. Biosens Bioelectron 2022; 216:114643. [PMID: 36030742 DOI: 10.1016/j.bios.2022.114643] [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: 02/28/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022]
Abstract
The transfer of redox-labelled bioelectrochemical sensors from proteins to cells is not straightforward because of the cell downward force issue on the surface of the sensors. In this paper, 20-nm-thick nanopillars are introduced to overcome this issue, in a well-controlled manner. We show on both molecular dynamics simulations and experiments that suspending cells a few nanometers above an electrode surface enables redox-labelled tethered DNA aptamer probes to move freely, while remaining at an interaction distance from a target membrane protein, i. e. epithelial cell adhesion molecule (EpCAM), which is typically overexpressed in cancer cells. By this nanopillar configuration, the interaction of aptamer with cancer cells is clearly observable, with 13 cells as the lower limit of detection. Nanoconfinement induced by the gap between the electrode surface and the cell membrane appears to improve the limit of detection and to lower the melting temperature of DNA aptamer hairpins, offering an additional degree of freedom to optimize molecular recognition mechanisms. This novel nanosupported electrochemical DNA cell sensor scheme including Brownian-fluctuating redox species opens new opportunities for the design of all-electrical sensors using redox-labelled probes.
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Affiliation(s)
- S Li
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan.
| | - Y Coffinier
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq Cedex, 59652, France
| | - C Lagadec
- Univ. Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - F Cleri
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq Cedex, 59652, France
| | - K Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, 3-1, Morinosato-Wakamiya, Atsugi-shi, 243-0198, Japan
| | - A Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, 3-1, Morinosato-Wakamiya, Atsugi-shi, 243-0198, Japan
| | - T Fujii
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - S-H Kim
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - N Clément
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan.
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Landuzzi F, Viader-Godoy X, Cleri F, Pastor I, Ritort F. Detection of single DNA mismatches by force spectroscopy in short DNA hairpins. J Chem Phys 2020; 152:074204. [PMID: 32087630 DOI: 10.1063/1.5139284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Identification of defective DNA structures is a difficult task, since small differences in base-pair bonding are hidden in the local structural variability of a generally random base-pair sequence. Defects, such as base mismatches, missing bases, crosslinks, and so on, occur in DNA with high frequency and must be efficiently identified and repaired to avoid dire consequences such as genetic mutations. Here, we focus on the detection of base mismatches, which is local deviations from the ideal Watson-Crick pairing rule, which may typically originate from DNA replication process, foreign chemical attack, or ionizing radiation. Experimental detection of a mismatch defect demands the ability to measure slight deviations in the free energy and molecular structure. We introduce different mismatches in short DNA hairpins (10 or 20 base pairs plus a 4-base loop) sandwiched between dsDNA handles to be used in single-molecule force spectroscopy with optical tweezers. We perform both hopping and force-pulling experiments to measure the excess free energies and deduce the characteristic kinetic signatures of the mismatch from the force-distance curves. All-atom molecular dynamics simulations lend support to the detailed interpretation of the experimental data. Such measurements, at the lowest sensitivity limits of this experimental technique, demonstrate the capability of identifying the presence of mismatches in a random complementary dsDNA sequence and provide lower bounds for the ability to distinguish different structural defects.
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Affiliation(s)
- F Landuzzi
- Department of Physics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Japan
| | - X Viader-Godoy
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - F Cleri
- I.E.M.N. (UMR Cnrs 8520), 59652 Villeneuve d'Ascq, France
| | - I Pastor
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - F Ritort
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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D’Angelo A, Cleri F, Marimbeau P, Salvatores M, Grouiller JP. Analysis of Sample and Fuel Pin Irradiation Experiments in Phénix for Basic Nuclear Data Validation. NUCL SCI ENG 2017. [DOI: 10.13182/nse90-a19189] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- A. D’Angelo
- ENEA, Casaccia Nuclear Research Centre, Dipartimento Reattori Veloci, S.P. Anguillarese Km 1 + 300, 0060 Casaccia (Roma) Italy
| | - F. Cleri
- ENEA, Casaccia Nuclear Research Centre, Dipartimento Reattori Veloci, S.P. Anguillarese Km 1 + 300, 0060 Casaccia (Roma) Italy
| | - P. Marimbeau
- Centre d'Etudes Nucléaires de Cadarache, Service de Physique des Reacteurs et du Cycle, Departement de Recherche Physique, 13108 St. Paul-lez-Durance, France
| | - M. Salvatores
- Centre d'Etudes Nucléaires de Cadarache, Service de Physique des Reacteurs et du Cycle, Departement de Recherche Physique, 13108 St. Paul-lez-Durance, France
| | - J. P. Grouiller
- Centre d'Etudes Nucléaires de Cadarache, Service de Physique des Reacteurs et du Cycle, Departement de Recherche Physique, 13108 St. Paul-lez-Durance, France
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Copie G, Biaye M, Diesinger H, Melin T, Krzeminski C, Cleri F. Deformation Localization in Molecular Layers Constrained between Self-Assembled Au Nanoparticles. Langmuir 2017; 33:2677-2687. [PMID: 28221811 DOI: 10.1021/acs.langmuir.7b00237] [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: 06/06/2023]
Abstract
The localized deformation of molecular monolayers constrained between the spherical surfaces of Au nanoparticles is studied by means of molecular dynamics simulations. Alkyl or polyethylene glycol long-chain molecules were homogeneously distributed over the curved Au surface, pushed against each other by repeated cycles of force relaxation and constant-volume equilibration at temperatures increasing from 50 to 300 K before being slowly quenched to near-zero temperature. Plots of minimum configurational energy can be obtained as a function of the nanoparticle distance, according to different directions of approach; therefore, such simulations describe a range of deformations, from perfectly uniaxial compression to a combination of compression and shear. Despite the relative rigidity of molecular backbones, the deformation is always found to be localized at the interface between the opposing molecular monolayers. We find that shorter ligands can be more densely packed on the surface but do no interdigitate upon compression; they respond to the applied force by bending and twisting, thus changing their conformation while remaining disjointed. On the contrary, longer ligands attain lower surface densities and can interprenetrate when the nanoparticles are compressed against each other; such molecules remain rather straight and benefit from the increased overlap to maximize the adhesion by dispersion forces. The apparent Young's and shear moduli of a dense nanostructure, composed of a triangular arrangement of identical MUDA-decorated Au nanoparticles, are found to be smaller than estimates indirectly deduced by atomic-force experiments but quite close to previous computer simulations of molecular monolayers on flat surfaces and of bulk nanoparticle assemblies.
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Affiliation(s)
- G Copie
- Institut d'Electronique, Microélectronique et Nanotechnologie (IEMN), CNRS UMR 8520, Université de Lille 1 Sciences et Technologies , Avenue Poincaré, 59652 Villeneuve d'Ascq, France
| | - M Biaye
- Institut d'Electronique, Microélectronique et Nanotechnologie (IEMN), CNRS UMR 8520, Université de Lille 1 Sciences et Technologies , Avenue Poincaré, 59652 Villeneuve d'Ascq, France
| | - H Diesinger
- Institut d'Electronique, Microélectronique et Nanotechnologie (IEMN), CNRS UMR 8520, Université de Lille 1 Sciences et Technologies , Avenue Poincaré, 59652 Villeneuve d'Ascq, France
| | - T Melin
- Institut d'Electronique, Microélectronique et Nanotechnologie (IEMN), CNRS UMR 8520, Université de Lille 1 Sciences et Technologies , Avenue Poincaré, 59652 Villeneuve d'Ascq, France
| | - C Krzeminski
- Institut d'Electronique, Microélectronique et Nanotechnologie (IEMN), CNRS UMR 8520, Université de Lille 1 Sciences et Technologies , Avenue Poincaré, 59652 Villeneuve d'Ascq, France
| | - F Cleri
- Institut d'Electronique, Microélectronique et Nanotechnologie (IEMN), CNRS UMR 8520, Université de Lille 1 Sciences et Technologies , Avenue Poincaré, 59652 Villeneuve d'Ascq, France
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Tomezak M, Abbadie C, Lartigau E, Cleri F. A biophysical model of cell evolution after cytotoxic treatments: Damage, repair and cell response. J Theor Biol 2015; 389:146-58. [PMID: 26549470 DOI: 10.1016/j.jtbi.2015.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 07/19/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 10/22/2022]
Abstract
We present a theoretical agent-based model of cell evolution under the action of cytotoxic treatments, such as radiotherapy or chemotherapy. The major features of cell cycle and proliferation, cell damage and repair, and chemical diffusion are included. Cell evolution is based on a discrete Markov chain, with cells stepping along a sequence of discrete internal states from 'normal' to 'inactive'. Probabilistic laws are introduced for each type of event a cell can undergo during its life: duplication, arrest, senescence, damage, reparation, or death. We adjust the model parameters on a series of cell irradiation experiments, carried out in a clinical LINAC, in which the damage and repair kinetics of single- and double-strand breaks are followed. Two showcase applications of the model are then presented. In the first one, we reconstruct the cell survival curves from a number of published low- and high-dose irradiation experiments. We reobtain a very good description of the data without assuming the well-known linear-quadratic model, but instead including a variable DSB repair probability. The repair capability of the model spontaneously saturates to an exponential decay at increasingly high doses. As a second test, we attempt to simulate the two extreme possibilities of the so-called 'bystander' effect in radiotherapy: the 'local' effect versus a 'global' effect, respectively activated by the short-range or long-range diffusion of some factor, presumably secreted by the irradiated cells. Even with an oversimplified simulation, we could demonstrate a sizeable difference in the proliferation rate of non-irradiated cells, the proliferation acceleration being much larger for the global than the local effect, for relatively small fractions of irradiated cells in the colony.
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Affiliation(s)
- M Tomezak
- Institut d׳Electronique Microelectronique et Nanotechnologie (IEMN), UMR Cnrs 8520, 59652 Villeneuve d׳Ascq, France; CNRS, Institut Pasteur de Lille, UMR Cnrs 8161 Mechanisms of Tumorigenesis and Targeted Therapies, 59000 Lille, France
| | - C Abbadie
- CNRS, Institut Pasteur de Lille, UMR Cnrs 8161 Mechanisms of Tumorigenesis and Targeted Therapies, 59000 Lille, France; Université de Lille I, Sciences et Technologies, 59650 Villeneuve d׳Ascq, France
| | - E Lartigau
- Centre de Lutte contre le Cancer "Oscar Lambret", 59000 Lille, France
| | - F Cleri
- Institut d׳Electronique Microelectronique et Nanotechnologie (IEMN), UMR Cnrs 8520, 59652 Villeneuve d׳Ascq, France; Université de Lille I, Sciences et Technologies, 59650 Villeneuve d׳Ascq, France.
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Prasher RS, Hu XJ, Chalopin Y, Mingo N, Lofgreen K, Volz S, Cleri F, Keblinski P. Turning carbon nanotubes from exceptional heat conductors into insulators. Phys Rev Lett 2009; 102:105901. [PMID: 19392127 DOI: 10.1103/physrevlett.102.105901] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Indexed: 05/27/2023]
Abstract
Thermal conductivity (kappa) of isolated carbon nanotubes (CNTs) is higher than the kappa of diamond; however, in this Letter we show that the kappa of a packed bed of three-dimensional random networks of single and multiwall CNTs is smaller than that of thermally insulating amorphous polymers. The thermoelectric power (Sigma) of the random network of CNTs was also measured. The Sigma of a single wall nanotube network is very similar to that of isolated nanotubes and, in contrast with kappa, Sigma shows a strong dependence on the tube diameter.
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Affiliation(s)
- Ravi S Prasher
- Department of Mechanical and Aerospace Engineering, Arizona State University, Tempe, Arizona, USA.
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Abstract
We investigate the physical meaning of the intrinsic crack resistance in the Griffith theory of brittle fracture by means of atomic-scale simulations. By taking cubic SiC as a typical brittle material, we show that the widely accepted identification of intrinsic crack resistance with the free surface energy underestimates the energy-release rate. The strain dependence of the Young modulus and surface energy, as well as allowance for lattice trapping, improve the estimate of the crack resistance. In the smallest scale limit, crack resistance can be fitted by an empirical elastoplastic model.
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Affiliation(s)
- A Mattoni
- INFM-SLACS Sardinian Laboratory for Computational Materials Science and Dipartimento di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Ca, Italy
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Cleri F, Mazzone G, Rosato V. Order-disorder transition in Cu3Au: A combined molecular-dynamics and cluster-variation-method approach. Phys Rev B Condens Matter 1993; 47:14541-14544. [PMID: 10005809 DOI: 10.1103/physrevb.47.14541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Benhar O, Cleri F. Stability of the ground state of finite nuclei against neutral pion condensation. Phys Rev C Nucl Phys 1986; 34:1134-1136. [PMID: 9953561 DOI: 10.1103/physrevc.34.1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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