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González A, Wildes AR, Mossou E, Cristiglio V, Moiroux G, Garden JL, Cuesta-López S, Theodorakopoulos N, Peyrard M. Melting transition of oriented Li-DNA fibers submerged in ethanol solutions. Biopolymers 2021; 112:e23422. [PMID: 33600618 DOI: 10.1002/bip.23422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/08/2021] [Accepted: 01/21/2021] [Indexed: 11/09/2022]
Abstract
The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water. They become weaker still and the DNA less stable as the ethanol concentration increases but, conversely, the fibers become more compact and the distances between base pairs become more regular. The results show that the melting transition is relatively insensitive to local confinement and depends more on the interaction between the DNA and its aqueous environment.
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Affiliation(s)
- Adrián González
- Institut Laue-Langevin, Grenoble, France.,ICCRAM, University of Burgos, Burgos, Spain.,Nano and Biophysics division, Department of Physics, Chalmers University of Technology, Göteborg, Sweden
| | | | | | | | - Gaël Moiroux
- Institut Néel, CNRS, Grenoble, France.,Institut Néel, University Grenoble Alpes, Grenoble, France
| | - Jean-Luc Garden
- Institut Néel, CNRS, Grenoble, France.,Institut Néel, University Grenoble Alpes, Grenoble, France
| | - Santiago Cuesta-López
- ICCRAM, University of Burgos, Burgos, Spain.,Advanced Materials and Computational Engineering, ICAMCyL Foundation International Center for Advanced Materials and Raw Materials of Castilla y León, León, Spain
| | - Nikos Theodorakopoulos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Athens, Greece.,Fachbereich Physik, Universität Konstanz, Constance, Germany
| | - Michel Peyrard
- Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique, CNRS, UMR 5672, Lyon, France
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Peyrard M, Garden JL. Memory effects in glasses: Insights into the thermodynamics of out-of-equilibrium systems revealed by a simple model of the Kovacs effect. Phys Rev E 2020; 102:052122. [PMID: 33327132 DOI: 10.1103/physreve.102.052122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/03/2020] [Indexed: 11/07/2022]
Abstract
Glasses are interesting materials because they allow us to explore the puzzling properties of out-of-equilibrium systems. One of them is the Kovacs effect in which a glass, brought to an out-of-equilibrium state in which all its thermodynamic variables are identical to those of an equilibrium state, nevertheless evolves, showing a hump in some global variable before the thermodynamic variables come back to their starting point. We show that a simple three-state system is sufficient to study this phenomenon using numerical integrations and exact analytical calculations. It also brings some light on the concept of fictive temperature, often used to extend standard thermodynamics to the out-of-equilibrium properties of glasses. We confirm that the concept of a unique fictive temperature is not valid, an show it can be extended to make a connection with the various relaxation processes in the system. The model also brings further insights on the thermodynamics of out-of-equilibrium systems. Moreover, we show that the three-state model is able to describe various effects observed in glasses such as the asymmetric relaxation to equilibrium discussed by Kovacs, or the reverse crossover measured on B_{2}O_{3}.
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Affiliation(s)
- Michel Peyrard
- Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique CNRS UMR 5672, 46 allée d'Italie, F-69364 Lyon Cedex 7, France
| | - Jean-Luc Garden
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NÉEL, 38000 Grenoble, France
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González A, Wildes A, Marty-Roda M, Cuesta-López S, Mossou E, Studer A, Demé B, Moiroux G, Garden JL, Theodorakopoulos N, Peyrard M. Melting Transition of Oriented DNA Fibers Submerged in Poly(ethylene glycol) Solutions Studied by Neutron Scattering and Calorimetry. J Phys Chem B 2018; 122:2504-2515. [DOI: 10.1021/acs.jpcb.7b11608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adrián González
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
- ICCRAM, University of Burgos, Plaza Misael Bañuelos, 09001 Burgos, Spain
| | - Andrew Wildes
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
| | - Marta Marty-Roda
- ICCRAM, University of Burgos, Plaza Misael Bañuelos, 09001 Burgos, Spain
| | | | - Estelle Mossou
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
- Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Andrew Studer
- ANSTO, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Bruno Demé
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
| | - Gaël Moiroux
- Institut Néel, University Grenoble Alpes, F-38042 Grenoble, France
- Institut Néel, CNRS, 25 Avenue des Martyrs, F-38042 Grenoble, France
| | - Jean-Luc Garden
- Institut Néel, University Grenoble Alpes, F-38042 Grenoble, France
- Institut Néel, CNRS, 25 Avenue des Martyrs, F-38042 Grenoble, France
| | - Nikos Theodorakopoulos
- Fachbereich Physik, Universität Konstanz, D-78457 Konstanz, Germany
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vasileos Constantinou 48, 116 35 Athens, Greece
| | - Michel Peyrard
- Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique, CNRS, UMR 5672, 46 allée d’Italie, F-69364 Lyon Cedex 7, France
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Wildes A, Khadeeva L, Trewby W, Valle-Orero J, Studer A, Garden JL, Peyrard M. Melting of Highly Oriented Fiber DNA Subjected to Osmotic Pressure. J Phys Chem B 2015; 119:4441-9. [DOI: 10.1021/acs.jpcb.5b01343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Wildes
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
| | - Liya Khadeeva
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
- Institut de Physique de Rennes, UMR UR1 - CNRS 6251, 35042 Rennes Cedex, France
| | - William Trewby
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
- Department
of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Jessica Valle-Orero
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew Studer
- ANSTO, Locked Bag 2001, Kirrawee
DC, NSW 2232, Australia
| | - Jean-Luc Garden
- CNRS, Institut
NÉEL, F-38042 Grenoble, France
- Université Grenoble Alpes, Inst NEEL, F-3800 Grenoble, France
| | - Michel Peyrard
- Laboratoire
de Physique, Ecole Normale Supérieure de Lyon, 46 Allée
d’Italie, 69364 Lyon Cedex 07, France
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Kahouli A, Valle-Orero J, Garden JL, Peyrard M. Ionic mobility in DNA films studied by dielectric spectroscopy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2014; 37:39. [PMID: 25260324 DOI: 10.1140/epje/i2014-14082-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/14/2014] [Accepted: 09/08/2014] [Indexed: 06/03/2023]
Abstract
Double-helix DNA molecules can be found under different conformational structures driven by ionic and hydration surroundings. Usually, only the B-form of DNA, which is the only form stable in aqueous solution, can be studied by dielectric measurements. Here, the dielectric responses of DNA molecules in the A- and B-form, oriented co-linearly within fibres assembled in a film have been analyzed. The dielectric dispersion, permittivity and dissipation factor, have been measured as a function of frequency, strength voltage, time, temperature and nature of the counter-ions. Besides a high electrode polarization component, two relaxation peaks have been observed and fitted by two Cole-Cole relaxation terms. In the frequency range that we investigated (0.1 Hz to 5 ·10(6) Hz) the dielectric properties are dominated by the mobility and diffusivity of the counter-ions and their interactions with the DNA molecules, which can therefore be characterized for the A- and B-forms of DNA.
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Affiliation(s)
- Abdelkader Kahouli
- Grenoble Electrical Engineering Laboratory (G2ELab), Université Joseph Fourier, 25 rue des Martyrs, 38042, Grenoble cedex 9, France
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Valle-Orero J, Wildes A, Garden JL, Peyrard M. Purification of A-Form DNA Fiber Samples by the Removal of B-Form DNA Residues. J Phys Chem B 2013; 117:1849-56. [DOI: 10.1021/jp311199f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jessica Valle-Orero
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Andrew Wildes
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Jean-Luc Garden
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP
166, 38042 Grenoble cedex 9, France
| | - Michel Peyrard
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée
d’Italie, 69364 Lyon Cedex 07, France
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