The Experts below are selected from a list of 8430 Experts worldwide ranked by ideXlab platform
Manoel Manghi - One of the best experts on this subject based on the ideXlab platform.
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dynamical control of denaturation bubble nucleation in supercoiled dna minicircles
Physical Review E, 2020Co-Authors: Francois Sicard, Nicolas Destainville, Philippe Rousseau, Catherine Tardin, Manoel ManghiAbstract: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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dna denaturation bubbles free energy landscape and nucleation closure rates
Journal of Chemical Physics, 2015Co-Authors: Francois Sicard, Nicolas Destainville, Manoel ManghiAbstract:The issue of the nucleation and slow closure mechanisms of non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (respectively, closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of 22 kBT (respectively, 13 kBT) at room temperature T. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the Millisecond Range. Contrary to small breathing bubbles, those more than 4 base-pair bubbles are of biological relevance, for example, when a pre-existing state of denaturation is required by specific DNA-binding proteins.
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dna denaturation bubbles free energy landscape and nucleation closure rates
arXiv: Soft Condensed Matter, 2014Co-Authors: Francois Sicard, Nicolas Destainville, Manoel ManghiAbstract:The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (resp. closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of $22~k_{\rm B}T$ (resp. $13~k_{\rm B}T$) at room temperature $T$. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the Millisecond Range. Contrary to small breathing bubbles, these more than 4~base-pair bubbles are of biological relevance, for example when a preexisting state of denaturation is required by specific DNA-binding proteins.
Francois Sicard - One of the best experts on this subject based on the ideXlab platform.
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dynamical control of denaturation bubble nucleation in supercoiled dna minicircles
Physical Review E, 2020Co-Authors: Francois Sicard, Nicolas Destainville, Philippe Rousseau, Catherine Tardin, Manoel ManghiAbstract: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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dna denaturation bubbles free energy landscape and nucleation closure rates
Journal of Chemical Physics, 2015Co-Authors: Francois Sicard, Nicolas Destainville, Manoel ManghiAbstract:The issue of the nucleation and slow closure mechanisms of non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (respectively, closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of 22 kBT (respectively, 13 kBT) at room temperature T. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the Millisecond Range. Contrary to small breathing bubbles, those more than 4 base-pair bubbles are of biological relevance, for example, when a pre-existing state of denaturation is required by specific DNA-binding proteins.
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dna denaturation bubbles free energy landscape and nucleation closure rates
arXiv: Soft Condensed Matter, 2014Co-Authors: Francois Sicard, Nicolas Destainville, Manoel ManghiAbstract:The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (resp. closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of $22~k_{\rm B}T$ (resp. $13~k_{\rm B}T$) at room temperature $T$. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the Millisecond Range. Contrary to small breathing bubbles, these more than 4~base-pair bubbles are of biological relevance, for example when a preexisting state of denaturation is required by specific DNA-binding proteins.
Nicolas Destainville - One of the best experts on this subject based on the ideXlab platform.
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dynamical control of denaturation bubble nucleation in supercoiled dna minicircles
Physical Review E, 2020Co-Authors: Francois Sicard, Nicolas Destainville, Philippe Rousseau, Catherine Tardin, Manoel ManghiAbstract: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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dna denaturation bubbles free energy landscape and nucleation closure rates
Journal of Chemical Physics, 2015Co-Authors: Francois Sicard, Nicolas Destainville, Manoel ManghiAbstract:The issue of the nucleation and slow closure mechanisms of non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (respectively, closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of 22 kBT (respectively, 13 kBT) at room temperature T. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the Millisecond Range. Contrary to small breathing bubbles, those more than 4 base-pair bubbles are of biological relevance, for example, when a pre-existing state of denaturation is required by specific DNA-binding proteins.
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dna denaturation bubbles free energy landscape and nucleation closure rates
arXiv: Soft Condensed Matter, 2014Co-Authors: Francois Sicard, Nicolas Destainville, Manoel ManghiAbstract:The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (resp. closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of $22~k_{\rm B}T$ (resp. $13~k_{\rm B}T$) at room temperature $T$. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the Millisecond Range. Contrary to small breathing bubbles, these more than 4~base-pair bubbles are of biological relevance, for example when a preexisting state of denaturation is required by specific DNA-binding proteins.
Claude Piguet - One of the best experts on this subject based on the ideXlab platform.
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extending lifetimes of lanthanide based nir emitters nd yb in the Millisecond Range through cr iii sensitization in discrete bimetallic edifices
Abstracts of Papers 227th ACS National Meeting Anaheim CA United States March 28-April 1 2004, 2004Co-Authors: Daniel Imbert, Martine Cantuel, Jeanclaude G Bunzli, Gerald Bernardinelli, Claude PiguetAbstract:Reference LCSL-CONF-2004-016View record in Web of Science Record created on 2006-02-15, modified on 2017-05-12
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extending lifetimes of lanthanide based near infrared emitters nd yb in the Millisecond Range through cr iii sensitization in discrete bimetallic edifices
Journal of the American Chemical Society, 2003Co-Authors: Daniel Imbert, Martine Cantuel, Jeanclaude G Bunzli, Gerald Bernardinelli, Claude PiguetAbstract:A [Cr(alpha,alpha'-diimine)3]3+ chromophore is used as a donor for sensitizing NdIII and YbIII near-infrared (NIR) emitters in the heterobimetallic helicates [LnCrIIIL3]6+. The intramolecular CrIII --> LnIII energy transfer process controls the population of the lanthanide-centered emitting levels, thus leading to unprecedented extension of the NIR luminescence decay times in the Millisecond Range for Nd and Yb ions incorporated in coordination complexes.
Daniel Imbert - One of the best experts on this subject based on the ideXlab platform.
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extending lifetimes of lanthanide based nir emitters nd yb in the Millisecond Range through cr iii sensitization in discrete bimetallic edifices
Abstracts of Papers 227th ACS National Meeting Anaheim CA United States March 28-April 1 2004, 2004Co-Authors: Daniel Imbert, Martine Cantuel, Jeanclaude G Bunzli, Gerald Bernardinelli, Claude PiguetAbstract:Reference LCSL-CONF-2004-016View record in Web of Science Record created on 2006-02-15, modified on 2017-05-12
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extending lifetimes of lanthanide based near infrared emitters nd yb in the Millisecond Range through cr iii sensitization in discrete bimetallic edifices
Journal of the American Chemical Society, 2003Co-Authors: Daniel Imbert, Martine Cantuel, Jeanclaude G Bunzli, Gerald Bernardinelli, Claude PiguetAbstract:A [Cr(alpha,alpha'-diimine)3]3+ chromophore is used as a donor for sensitizing NdIII and YbIII near-infrared (NIR) emitters in the heterobimetallic helicates [LnCrIIIL3]6+. The intramolecular CrIII --> LnIII energy transfer process controls the population of the lanthanide-centered emitting levels, thus leading to unprecedented extension of the NIR luminescence decay times in the Millisecond Range for Nd and Yb ions incorporated in coordination complexes.