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Soukarié D, Rousseau P, Salhi M, de Caro A, Escudier JM, Tardin C, Ecochard V, Salomé L. Single-Molecule Sandwich Aptasensing on Nanoarrays by Tethered Particle Motion Analysis. Anal Chem 2022; 94:4319-4327. [PMID: 35226451 DOI: 10.1021/acs.analchem.1c04995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput single-molecule techniques are expected to challenge the demand for rapid, simple, and sensitive detection methods in health and environmental fields. Based on a single-DNA-molecule biochip for the parallelization of tethered particle motion analyses by videomicroscopy coupled to image analysis and its smart combination with aptamers, we successfully developed an aptasensor enabling the detection of single target molecules by a sandwich assay. One aptamer is grafted to the nanoparticles tethered to the surface by a long DNA molecule bearing the second aptamer in its middle. The detection and quantification of the target are direct. The recognition of the target by a pair of aptamers leads to a looped configuration of the DNA-particle complex associated with a restricted motion of the particles, which is monitored in real time. An analytical range extending over 3 orders of magnitude of target concentration with a limit of detection in the picomolar range was obtained for thrombin.
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Affiliation(s)
- Diana Soukarié
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Philippe Rousseau
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Maya Salhi
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Alexia de Caro
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Vincent Ecochard
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
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2
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Mizuno D, Tardin C, Schmidt CF. Rapid local compression in active gels is caused by nonlinear network response. Soft Matter 2020; 16:9369-9382. [PMID: 32945304 DOI: 10.1039/c9sm02362c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The actin cytoskeleton in living cells generates forces in conjunction with myosin motor proteins to directly and indirectly drive essential cellular processes. The semiflexible filaments of the cytoskeleton can respond nonlinearly to the collective action of motors. We here investigate mechanics and force generation in a model actin cytoskeleton, reconstituted in vitro, by observing the response and fluctuations of embedded micron-scale probe particles. Myosin mini-filaments can be modeled as force dipoles and give rise to deformations in the surrounding network of cross-linked actin. Anomalously correlated probe fluctuations indicate the presence of rapid local compression or draining of the network that emerges in addition to the ordinary linear shear elastic (incompressible) response to force dipoles. The anomalous propagation of compression can be attributed to the nonlinear response of actin filaments to the microscopic forces, and is quantitatively consistent with motor-generated large-scale stiffening of the gels.
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Affiliation(s)
- D Mizuno
- Department of Physics, Kyushu University, 819-0395 Fukuoka, Japan
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3
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Abstract
The occurrence of pharmaceutical residues in surface water is raising environmental concern. To accompany the evolution of measures for natural resources protection, sensing methods enabling sensitive and rapid water quality monitoring are needed. We recently managed the parallelization of the Tethered Particle Motion (TPM), a single molecule technique, sensitive to the conformational changes of DNA. Here, we investigate the capacity of high throughput TPM (htTPM) to detect drugs that intercalate into DNA. As a proof-of-concept we analyze the htTPM signal for two DNA intercalating dyes, namely, YOYO-1 and SYTOX orange. The efficient detection of intercalating drugs is then demonstrated with doxorubicin. We further evaluate the possibility to detect carbamazepine, an antiepileptic massively prescribed and persistent in water, which had been described to interact with DNA through intercalation. Our results corroborated by other techniques show that, in fact, carbamazepine is not a DNA intercalator. The comparison of the results obtained with different aqueous buffers and solutions allows us to identify optimal conditions for the monitoring of intercalation compounds by htTPM.
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Affiliation(s)
- Sandra Serres
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
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Sicard F, Destainville N, Rousseau P, Tardin C, Manghi M. Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles. Phys Rev E 2020; 101:012403. [PMID: 32069623 DOI: 10.1103/physreve.101.012403] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Indexed: 06/10/2023]
Abstract
We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.
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Affiliation(s)
- François Sicard
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Nicolas Destainville
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génetique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Catherine Tardin
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
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5
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Lavelle C, Tardin C. Single molecule approaches of nucleic acids conformational changes. Methods 2019; 169:1-2. [PMID: 31518659 DOI: 10.1016/j.ymeth.2019.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Christophe Lavelle
- National Museum of Natural History, CNRS, UMR7196 / INSERM U1164, 75005 Paris, France.
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Brunet A, Salomé L, Rousseau P, Destainville N, Manghi M, Tardin C. How does temperature impact the conformation of single DNA molecules below melting temperature? Nucleic Acids Res 2019; 46:2074-2081. [PMID: 29294104 PMCID: PMC5829751 DOI: 10.1093/nar/gkx1285] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/19/2017] [Indexed: 01/26/2023] Open
Abstract
The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription during which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting this idea, different biophysical studies have found an unexpected increase in the flexibility of DNA molecules with various sequences as a function of the temperature, which would be consistent with the formation of a growing number of locally denatured sequences. Here, we take advantage of our capacity to detect subtle changes occurring on DNA by using high throughput tethered particle motion to question the existence of bubbles in double stranded DNA under physiological salt conditions through their conformational impact on DNA molecules ranging from several hundreds to thousands of base pairs. Our results strikingly differ from previously published ones, as we do not detect any unexpected change in DNA flexibility below melting temperature. Instead, we measure a bending modulus that remains stable with temperature as expected for intact double stranded DNA.
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Affiliation(s)
- Annaël Brunet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.,Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
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Guilbaud S, Salomé L, Destainville N, Manghi M, Tardin C. Dependence of DNA Persistence Length on Ionic Strength and Ion Type. Phys Rev Lett 2019; 122:028102. [PMID: 30720315 DOI: 10.1103/physrevlett.122.028102] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 06/09/2023]
Abstract
Even though the persistence length L_{P} of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength I lacks a consensual description. Using a high-throughput single-molecule technique and statistical physics modeling, we measure L_{P} in the presence of monovalent (Li^{+}, Na^{+}, K^{+}) and divalent (Mg^{2+}, Ca^{2+}) metallic and alkyl ammonium ions, over a large range 0.5 mM≤I≤5 M. We show that linear Debye-Hückel-type theories do not describe even part of these data. By contrast, the Netz-Orland and Trizac-Shen formulas, two approximate theories including nonlinear electrostatic effects and the finite DNA radius, fit our data with divalent and monovalent ions, respectively, over the whole I range. Furthermore, the metallic ion type does not influence L_{P}(I), in contrast to alkyl ammonium monovalent ions at high I.
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Affiliation(s)
- Sébastien Guilbaud
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31 077 Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31 077 Toulouse, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, 31 062 Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, 31 062 Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31 077 Toulouse, France
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Abstract
Protein-induced DNA bridging and looping is a common mechanism for various and essential processes in bacterial chromosomes. This mechanism is preserved despite the very different bacterial conditions and their expected influence on the thermodynamic and kinetic characteristics of the bridge formation and stability. Over the last two decades, single-molecule techniques carried out on in vitro DNA systems have yielded valuable results which, in combination with theoretical works, have clarified the effects of different parameters of nucleoprotein complexes on the protein-induced DNA bridging and looping process. In this review, I will outline the features that can be measured for such processes with various single-molecule techniques in use in the field. I will then describe both the experimental results and the theoretical models that illuminate the contribution of the DNA molecule itself as well as that of the bridging proteins in the DNA looping mechanism at play in the nucleoid of E. coli.
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Affiliation(s)
- Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.
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Brunet A, Chevalier S, Destainville N, Manghi M, Rousseau P, Salhi M, Salome L, Tardin C. Probing a Label-Free Local Bend in DNA by Single Molecule Tethered Particle Motion. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1027] [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] Open
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Brunet A, Tardin C, Salome L, Rousseau P, Destainville N, Manghi M. Dependence of DNA Persistence Length on Ionic Strength of Solutions with Monovalent and Divalent Salts: A Joint Theory–Experiment Study. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2175] [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: 10/22/2022] Open
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11
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Brunet A, Tardin C, Salomé L, Rousseau P, Destainville N, Manghi M. Dependence of DNA Persistence Length on Ionic Strength of Solutions with Monovalent and Divalent Salts: A Joint Theory–Experiment Study. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00735] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annaël Brunet
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) 205 route de Narbonne, BP 64182, F-31077 Toulouse, France
- UPS,
IPBS, Université de Toulouse F-31077 Toulouse, France
- UPS, Laboratoire
de Physique Théorique (IRSAMC), Université de Toulouse, F-31062 Toulouse, France
- CNRS, Laboratoire de Physique Théorique (IRSAMC), F-31062 Toulouse, France
| | - Catherine Tardin
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) 205 route de Narbonne, BP 64182, F-31077 Toulouse, France
- UPS,
IPBS, Université de Toulouse F-31077 Toulouse, France
| | - Laurence Salomé
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) 205 route de Narbonne, BP 64182, F-31077 Toulouse, France
- UPS,
IPBS, Université de Toulouse F-31077 Toulouse, France
| | - Philippe Rousseau
- UPS,
Laboratoire de Microbiologie et Génétique Moléculaires
(LMGM), Université de Toulouse, F-31062 Toulouse, France
- CNRS, LMGM, UMR CNRS-UPS 5100, F-31062 Toulouse, France
| | - Nicolas Destainville
- UPS, Laboratoire
de Physique Théorique (IRSAMC), Université de Toulouse, F-31062 Toulouse, France
- CNRS, Laboratoire de Physique Théorique (IRSAMC), F-31062 Toulouse, France
| | - Manoel Manghi
- UPS, Laboratoire
de Physique Théorique (IRSAMC), Université de Toulouse, F-31062 Toulouse, France
- CNRS, Laboratoire de Physique Théorique (IRSAMC), F-31062 Toulouse, France
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12
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Brunet A, Chevalier S, Destainville N, Manghi M, Rousseau P, Salhi M, Salomé L, Tardin C. Probing a label-free local bend in DNA by single molecule tethered particle motion. Nucleic Acids Res 2015; 43:e72. [PMID: 25765645 PMCID: PMC4477641 DOI: 10.1093/nar/gkv201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/01/2015] [Indexed: 02/07/2023] Open
Abstract
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.
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Affiliation(s)
- Annaël Brunet
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Sébastien Chevalier
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Nicolas Destainville
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Manoel Manghi
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Philippe Rousseau
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Maya Salhi
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Laurence Salomé
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Catherine Tardin
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
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Abstract
Microdomains corresponding to localized partition of lipids between ordered and less ordered environments are the subject of intensive investigations, because of their putative participation in modulating cellular responses. One popular approach in the field consists in labelling membranes with solvatochromic fluorescent probes such as laurdan and C-laurdan. In this report, we describe a high-yield procedure for the synthesis of laurdan, C-laurdan and two new fluorophores, called MoC-laurdan and M-laurdan, as well as their extensive photophysical characterization. We find that the latter probe, M-laurdan, is particularly suited to discriminate lipid phases independently of the chemical nature of the lipids, as measured by both fluorescence Generalized Polarization (GP) and anisotropy in large unilamellar vesicles made of various lipid compositions. In addition, staining of live cells with M-laurdan shows a good stability over time without any apparent toxicity, as well as a wider distribution in the various cell compartments than the other probes.
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Affiliation(s)
- Serge Mazeres
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Université de Toulouse, Toulouse, F-31077, France
| | - Etienne Joly
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Université de Toulouse, Toulouse, F-31077, France
| | - Andre Lopez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Université de Toulouse, Toulouse, F-31077, France
| | - Catherine Tardin
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Université de Toulouse, Toulouse, F-31077, France
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14
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Diagne CT, Salhi M, Crozat E, Salomé L, Cornet F, Rousseau P, Tardin C. TPM analyses reveal that FtsK contributes both to the assembly and the activation of the XerCD-dif recombination synapse. Nucleic Acids Res 2013; 42:1721-32. [PMID: 24214995 PMCID: PMC3919580 DOI: 10.1093/nar/gkt1024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Circular chromosomes can form dimers during replication and failure to resolve those into monomers prevents chromosome segregation, which leads to cell death. Dimer resolution is catalysed by a highly conserved site-specific recombination system, called XerCD-dif in Escherichia coli. Recombination is activated by the DNA translocase FtsK, which is associated with the division septum, and is thought to contribute to the assembly of the XerCD-dif synapse. In our study, direct observation of the assembly of the XerCD-dif synapse, which had previously eluded other methods, was made possible by the use of Tethered Particle Motion, a single molecule approach. We show that XerC, XerD and two dif sites suffice for the assembly of XerCD-dif synapses in absence of FtsK, but lead to inactive XerCD-dif synapses. We also show that the presence of the γ domain of FtsK increases the rate of synapse formation and convert them into active synapses where recombination occurs. Our results represent the first direct observation of the formation of the XerCD-dif recombination synapse and its activation by FtsK.
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Affiliation(s)
- Cheikh Tidiane Diagne
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France, Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France, Université de Toulouse; UPS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); F-31062 Toulouse, France and CNRS; LMGM; F-31062 Toulouse, France
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15
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Plénat T, Tardin C, Rousseau P, Salomé L. High-throughput single-molecule analysis of DNA-protein interactions by tethered particle motion. Nucleic Acids Res 2012; 40:e89. [PMID: 22422843 PMCID: PMC3384352 DOI: 10.1093/nar/gks250] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [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: 01/20/2012] [Revised: 02/21/2012] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
Tethered particle motion (TPM) monitors the variations in the effective length of a single DNA molecule by tracking the Brownian motion of a bead tethered to a support by the DNA molecule. Providing information about DNA conformations in real time, this technique enables a refined characterization of DNA-protein interactions. To increase the output of this powerful but time-consuming single-molecule assay, we have developed a biochip for the simultaneous acquisition of data from more than 500 single DNA molecules. The controlled positioning of individual DNA molecules is achieved by self-assembly on nanoscale arrays fabricated through a standard microcontact printing method. We demonstrate the capacity of our biochip to study biological processes by applying our method to explore the enzymatic activity of the T7 bacteriophage exonuclease. Our single molecule observations shed new light on its behaviour that had only been examined in bulk assays previously and, more specifically, on its processivity.
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Affiliation(s)
- Thomas Plénat
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Catherine Tardin
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Philippe Rousseau
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Laurence Salomé
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
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16
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Plenat T, Tardin C, Rousseau P, Salome L. High-Throughput Single-Molecule Analysis of Nucleic Acid Enzyme Activity by Tethered Particle Motion. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2095] [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] Open
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17
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Comesaña-Hermo M, Estivill R, Ciuculescu D, Amiens C, Farle M, Batat P, Jonusauskas G, McClenaghan ND, Lecante P, Tardin C, Mazeres S. Photomodulation of the magnetisation of Co nanocrystals decorated with rhodamine B. Chemphyschem 2011; 12:2915-9. [PMID: 21976370 DOI: 10.1002/cphc.201100616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Miguel Comesaña-Hermo
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, 31077 Toulouse, France
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18
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Manghi M, Tardin C, Baglio J, Rousseau P, Salomé L, Destainville N. Probing DNA conformational changes with high temporal resolution by tethered particle motion. Phys Biol 2010; 7:046003. [PMID: 20952812 DOI: 10.1088/1478-3975/7/4/046003] [Citation(s) in RCA: 31] [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] [Indexed: 11/12/2022]
Abstract
The tethered particle motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150 nm). Notably we demonstrate that, for a particle of radius 20 nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20 ms.
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Affiliation(s)
- Manoel Manghi
- Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), F-31062 Toulouse, France. CNRS, F-31062 Toulouse, France
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19
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Rousseau P, Tardin C, Tolou N, Salomé L, Chandler M. A model for the molecular organisation of the IS911 transpososome. Mob DNA 2010; 1:16. [PMID: 20553579 PMCID: PMC2909936 DOI: 10.1186/1759-8753-1-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 06/16/2010] [Indexed: 11/10/2022] Open
Abstract
Tight regulation of transposition activity is essential to limit damage transposons may cause by generating potentially lethal DNA rearrangements. Assembly of a bona fide protein-DNA complex, the transpososome, within which transposition is catalysed, is a crucial checkpoint in this regulation. In the case of IS911, a member of the large IS3 bacterial insertion sequence family, the transpososome (synaptic complex A; SCA) is composed of the right and left inverted repeated DNA sequences (IRR and IRL) bridged by the transposase, OrfAB (the IS911-encoded enzyme that catalyses transposition). To characterise further this important protein-DNA complex in vitro, we used different tagged and/or truncated transposase forms and analysed their interaction with IS911 ends using gel electrophoresis. Our results allow us to propose a model in which SCA is assembled with a dimeric form of the transposase. Furthermore, we present atomic force microscopy results showing that the terminal inverted repeat sequences are probably assembled in a parallel configuration within the SCA. These results represent the first step in the structural description of the IS911 transpososome, and are discussed in comparison with the very few other transpososome examples described in the literature.
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Affiliation(s)
- Philippe Rousseau
- Centre National de la Recherche Scientifique, LMGM, F-31000 Toulouse, France.
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20
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Tardin C, Manghi M, Baglio J, Salome L, Destainville N. Influence of the Experimental Set-Up on Single Molecule DNA Dynamics When Analyzed by Tethered Particle Motion. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.985] [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: 10/19/2022] Open
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21
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Abstract
Cells actively probe mechanical properties of their environment by exerting internally generated forces. The response they encounter profoundly affects their behavior. Here we measure in a simple geometry the forces a cell exerts suspended by two optical traps. Our assay quantifies both the overall force and the fraction of that force transmitted to the environment. Mimicking environments of varying stiffness by adjusting the strength of the traps, we found that the force transmission is highly dependent on external compliance. This suggests a calibration mechanism for cellular mechanosensing.
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Affiliation(s)
- Daisuke Mizuno
- Organization for the Promotion of Advanced Research, Kyushu University, 812-8581 Fukuoka, Japan
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22
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Cognet L, Tardin C, Négrier MLM, Breillat C, Coussen F, Choquet D, Lounis B. Robust single-molecule approach for counting autofluorescent proteins. J Biomed Opt 2008; 13:031216. [PMID: 18601540 DOI: 10.1117/1.2940600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Using single-molecule microscopy, we present a method to quantify the number of single autofluorescent proteins when they cannot be optically resolved. This method relies on the measurement of the total intensity emitted by each aggregate until it photobleaches. This strategy overcomes the inherent problem of blinking of green fluorescent proteins. In the case of small protein aggregates, our method permits us to describe the mean composition with a precision of one protein. For aggregates containing a large number of proteins, it gives access to the average number of proteins gathered and a signature of the inhomogeneity of the aggregates' population. We applied this methodology to the quantification of small purified citrine multimers.
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Affiliation(s)
- Laurent Cognet
- Universite Bordeaux, Centre de Physique Moleculaire Optique et Hertzienne, Centre National de la Recherche Scientifique, 351 Cours de la Liberation, 33405 Talence, France.
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23
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Abstract
Cells both actively generate and sensitively react to forces through their mechanical framework, the cytoskeleton, which is a nonequilibrium composite material including polymers and motor proteins. We measured the dynamics and mechanical properties of a simple three-component model system consisting of myosin II, actin filaments, and cross-linkers. In this system, stresses arising from motor activity controlled the cytoskeletal network mechanics, increasing stiffness by a factor of nearly 100 and qualitatively changing the viscoelastic response of the network in an adenosine triphosphate-dependent manner. We present a quantitative theoretical model connecting the large-scale properties of this active gel to molecular force generation.
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Affiliation(s)
- Daisuke Mizuno
- Department of Physics and Astronomy, Vrije Universiteit, 1081HV Amsterdam, Netherlands
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24
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Cognet L, Tardin C, Boyer D, Choquet D, Tamarat P, Lounis B. Single metallic nanoparticle imaging for protein detection in cells. Proc Natl Acad Sci U S A 2003; 100:11350-5. [PMID: 13679586 PMCID: PMC208760 DOI: 10.1073/pnas.1534635100] [Citation(s) in RCA: 192] [Impact Index Per Article: 9.1] [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: 06/11/2003] [Indexed: 11/18/2022] Open
Abstract
We performed a visualization of membrane proteins labeled with 10-nm gold nanoparticles in cells, using an all-optical method based on photothermal interference contrast. The high sensitivity of the method and the stability of the signals allows 3D imaging of individual nanoparticles without the drawbacks of photobleaching and blinking inherent to fluorescent markers. A simple analytical model is derived to account for the measurements of the signal amplitude and the spatial resolution. The photothermal interference contrast method provides an efficient, reproducible, and promising way to visualize low amounts of proteins in cells by optical means.
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Affiliation(s)
- L Cognet
- Centre de Physique Moléculaire Optique et Hertzienne, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5798 et Université Bordeaux 1, 351 Cours de la Libération, 33405 Talence, France
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25
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Abstract
Trafficking of AMPA receptors in and out of synapses is crucial for synaptic plasticity. Previous studies have focused on the role of endo/exocytosis processes or that of lateral diffusion of extra-synaptic receptors. We have now directly imaged AMPAR movements inside and outside synapses of live neurons using single-molecule fluorescence microscopy. Inside individual synapses, we found immobile and mobile receptors, which display restricted diffusion. Extra-synaptic receptors display free diffusion. Receptors could also exchange between these membrane compartments through lateral diffusion. Glutamate application increased both receptor mobility inside synapses and the fraction of mobile receptors present in a juxtasynaptic region. Block of inhibitory transmission to favor excitatory synaptic activity induced a transient increase in the fraction of mobile receptors and a decrease in the proportion of juxtasynaptic receptors. Altogether, our data show that rapid exchange of receptors between a synaptic and extra-synaptic localization occurs through regulation of receptor diffusion inside synapses.
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Affiliation(s)
- Catherine Tardin
- Centre de Physique Moléculaire Optique et Hertzienne - CNRS UMR 5798 et Université Bordeaux 1, 351 Cours de la Libération, 33405 Talence, France
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26
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Simon JM, Comastri SA, Tardin C. Multilocalization and the van Cittert-Zernike theorem. 2. Application to the Wollaston prism. J Opt Soc Am A Opt Image Sci Vis 2000; 17:1277-1283. [PMID: 10883980 DOI: 10.1364/josaa.17.001277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The van Cittert-Zernike theorem can be used to evaluate visibility at the exit of an amplitude-division interferometer with two-beam interferences. If the source illuminating the interferometer is a periodic array of slits, at the exit there is a sequence of localization surfaces. The formulas for the position and fringe spacing of the principal localization surfaces are applied to a Wollaston quartz prism, and there is good agreement between theoretical and experimental results. Moreover, the fringe localization depth and the intermediate localization surfaces obtained experimentally coincide with those predicted by theory.
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Affiliation(s)
- JM Simon
- Laboratorio de Optica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
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27
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Comastri SA, Simon JM, Tardin C. Multilocalization and the van Cittert-Zernike theorem. 1. Theory. J Opt Soc Am A Opt Image Sci Vis 2000; 17:1265-1276. [PMID: 10883979 DOI: 10.1364/josaa.17.001265] [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: 05/23/2023]
Abstract
The complex degree of coherence and the resulting van Cittert-Zernike theorem are employed to analyze the exit of an arbitrary amplitude-division interferometer with two-beam interferences. Considering that the source is a periodic array of spatially incoherent slits and assuming negligible equivalent aberrations and no vignetting, an expression for the complex degree of coherence as a function of the position of an exit point is derived. Formulas for the location, fringe spacing, and fringe localization depth of the multilocalized fringes are given.
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Affiliation(s)
- SA Comastri
- Laboratorio de Optica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina.
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