The Experts below are selected from a list of 288 Experts worldwide ranked by ideXlab platform

Helena M. G. Correia - One of the best experts on this subject based on the ideXlab platform.

  • Electric field induced charge transfer through single- and Double-Stranded DNA polymer molecules
    Soft Matter, 2011
    Co-Authors: Marta M. D. Ramos, Helena M. G. Correia
    Abstract:

    The charge transfer through single-stranded and Double-Stranded DNA polymer molecules has been the subject of numerous experimental and theoretical studies concerning their applications in molecular electronics. However, the underlying mechanisms responsible for their different electrical conductivity observed in the experiments are poorly understood. Here we use a self-consistent quantum molecular dynamics method to study the effect of an applied electric field along the molecular axis on charge transfer through single-stranded and Double-Stranded DNA polymer molecules with an injected electron or hole and assess the consequences for electronic applications. Charge transfer through both single-stranded and Double-Stranded DNA polymer molecules is predicted, regardless of the sign of the injected charge, the molecular structure and the base sequence. The amount of charge transfer through a Double-Stranded DNA polymer molecule is slightly lower than through the corresponding two isolated single-strands as a result of the lower charge transport through the purine–pyrimidine base-stacking as compared with through DNA nucleobase-stacking. These results suggest that each DNA polymer strand can act as a molecular wire with both the sugar–phosphate backbone and the bases playing an important role in charge transfer, which opens new perspectives for molecular electronics applications.

  • Electric field induced charge transfer through single- and Double-Stranded DNA polymer molecules
    Soft Matter, 2011
    Co-Authors: Marta M. D. Ramos, Helena M. G. Correia
    Abstract:

    The charge transfer through single-stranded and Double-Stranded DNA polymer molecules has been the subject of numerous experimental and theoretical studies concerning their applications in molecular electronics. However, the underlying mechanisms responsible for their different electrical conductivity observed in the experiments are poorly understood. Here we use a self-consistent quantum molecular dynamics method to study the effect of an applied electric field along the molecular axis on charge transfer through single-stranded and Double-Stranded DNA polymer molecules with an injected electron or hole and assess the consequences for electronic applications. Charge transfer through both single-stranded and Double-Stranded DNA polymer molecules is predicted, regardless of the sign of the injected charge, the molecular structure and the base sequence. The amount of charge transfer through a Double-Stranded DNA polymer molecule is slightly lower than through the corresponding two isolated single-strands as a result of the lower charge transport through the purine-pyrimidine base-stacking as compared with through DNA nucleobase-stacking. These results suggest that each DNA polymer strand can act as a molecular wire with both the sugar-phosphate backbone and the bases playing an important role in charge transfer, which opens new perspectives for molecular electronics applications.In this work, the calculations were performed on SeARCH (Services & Advanced Computing with HTC/HPC) funded FEDER funds through COMPETE program and by the Portuguese Foundation for Science and Technology (FCT) funds, under contract CONC-REEQ/443/EEI/2005,. One of us (H.M.G.C.) is also indebted to FCT for financial support under the post-doctoral grant no. SFRH/BPD/64554/2009

Christophe Escudé - One of the best experts on this subject based on the ideXlab platform.

  • Stem–loop oligonucleotides as tools for labelling double‐stranded DNA
    FEBS Journal, 2005
    Co-Authors: Bénédicte Géron-landre, Thibaut Roulon, Christophe Escudé
    Abstract:

    We report on a sequence-specific Double-Stranded DNA labelling strategy in which a stem–loop triplex forming oligonucleotide (TFO) is able to encircle its DNA target. Ligation of this TFO to either a short hairpin oligonucleotide or a long Double-Stranded DNA fragment leads to the formation of a topological complex. This process requires the hybridization of both extremities of the TFO to each other on a few base pairs. The effects of different factors on the formation of these complexes have been investigated. Efficient complex formation was observed using both GT or TC TFOs. The stem–loop structure enhances the specificity of the complex. The topologically linked TFO remains associated with its target even under conditions that do not favour triple-helix formation. This approach is sufficiently sensitive for detection of a 20-bp target sequence at the subfemtomolar level. This study provides new insights into the mechanics and properties of stem–loop TFOs and their complexes with Double-Stranded DNA targets. It emphasizes the interest of such molecules in the development of new tools for the specific labelling of short DNA sequences.

  • Stem–loop oligonucleotides as tools for labelling Double-Stranded DNA
    The FEBS journal, 2005
    Co-Authors: Bénédicte Géron-landre, Thibaut Roulon, Christophe Escudé
    Abstract:

    We report on a sequence-specific Double-Stranded DNA labelling strategy in which a stem-loop triplex forming oligonucleotide (TFO) is able to encircle its DNA target. Ligation of this TFO to either a short hairpin oligonucleotide or a long Double-Stranded DNA fragment leads to the formation of a topological complex. This process requires the hybridization of both extremities of the TFO to each other on a few base pairs. The effects of different factors on the formation of these complexes have been investigated. Efficient complex formation was observed using both GT or TC TFOs. The stem-loop structure enhances the specificity of the complex. The topologically linked TFO remains associated with its target even under conditions that do not favour triple-helix formation. This approach is sufficiently sensitive for detection of a 20-bp target sequence at the subfemtomolar level. This study provides new insights into the mechanics and properties of stem-loop TFOs and their complexes with Double-Stranded DNA targets. It emphasizes the interest of such molecules in the development of new tools for the specific labelling of short DNA sequences.

Marta M. D. Ramos - One of the best experts on this subject based on the ideXlab platform.

  • Electric field induced charge transfer through single- and Double-Stranded DNA polymer molecules
    Soft Matter, 2011
    Co-Authors: Marta M. D. Ramos, Helena M. G. Correia
    Abstract:

    The charge transfer through single-stranded and Double-Stranded DNA polymer molecules has been the subject of numerous experimental and theoretical studies concerning their applications in molecular electronics. However, the underlying mechanisms responsible for their different electrical conductivity observed in the experiments are poorly understood. Here we use a self-consistent quantum molecular dynamics method to study the effect of an applied electric field along the molecular axis on charge transfer through single-stranded and Double-Stranded DNA polymer molecules with an injected electron or hole and assess the consequences for electronic applications. Charge transfer through both single-stranded and Double-Stranded DNA polymer molecules is predicted, regardless of the sign of the injected charge, the molecular structure and the base sequence. The amount of charge transfer through a Double-Stranded DNA polymer molecule is slightly lower than through the corresponding two isolated single-strands as a result of the lower charge transport through the purine–pyrimidine base-stacking as compared with through DNA nucleobase-stacking. These results suggest that each DNA polymer strand can act as a molecular wire with both the sugar–phosphate backbone and the bases playing an important role in charge transfer, which opens new perspectives for molecular electronics applications.

  • Electric field induced charge transfer through single- and Double-Stranded DNA polymer molecules
    Soft Matter, 2011
    Co-Authors: Marta M. D. Ramos, Helena M. G. Correia
    Abstract:

    The charge transfer through single-stranded and Double-Stranded DNA polymer molecules has been the subject of numerous experimental and theoretical studies concerning their applications in molecular electronics. However, the underlying mechanisms responsible for their different electrical conductivity observed in the experiments are poorly understood. Here we use a self-consistent quantum molecular dynamics method to study the effect of an applied electric field along the molecular axis on charge transfer through single-stranded and Double-Stranded DNA polymer molecules with an injected electron or hole and assess the consequences for electronic applications. Charge transfer through both single-stranded and Double-Stranded DNA polymer molecules is predicted, regardless of the sign of the injected charge, the molecular structure and the base sequence. The amount of charge transfer through a Double-Stranded DNA polymer molecule is slightly lower than through the corresponding two isolated single-strands as a result of the lower charge transport through the purine-pyrimidine base-stacking as compared with through DNA nucleobase-stacking. These results suggest that each DNA polymer strand can act as a molecular wire with both the sugar-phosphate backbone and the bases playing an important role in charge transfer, which opens new perspectives for molecular electronics applications.In this work, the calculations were performed on SeARCH (Services & Advanced Computing with HTC/HPC) funded FEDER funds through COMPETE program and by the Portuguese Foundation for Science and Technology (FCT) funds, under contract CONC-REEQ/443/EEI/2005,. One of us (H.M.G.C.) is also indebted to FCT for financial support under the post-doctoral grant no. SFRH/BPD/64554/2009

Yashwant Singh - One of the best experts on this subject based on the ideXlab platform.

  • Shear unzipping of Double-Stranded DNA.
    Physical Review E, 2011
    Co-Authors: Shikha Prakash, Yashwant Singh
    Abstract:

    We propose a simple nonlinear scaler displacement model to calculate the distribution of effect created by a shear stress on a double stranded DNA (dsDNA) molecule and the value of shear force $F_c$ which is required to separate the two strands of a molecule. It is shown that as long as the force pulls entire strand in the direction of its application the value of $F_c$ depends linearly on the length; the deviation from linear behaviour takes place when part of a strand moves in opposite direction under the influence of force acting on the other strand. The calculated values of $F_c$ as a function of length of dsDNA molecules are in very good agreement with the experimental values of Hatch et al (Phys. Rev. E $\bf 78$, 011920 (2008)).

  • Shear unzipping of Double-Stranded DNA.
    Physical review. E Statistical nonlinear and soft matter physics, 2011
    Co-Authors: Shikha Prakash, Yashwant Singh
    Abstract:

    We use a simple nonlinear scaler displacement model to calculate the distribution of effects created by a shear stress on a Double-Stranded DNA (dsDNA) molecule and the value of shear force F(c) that is required to separate the two strands of a molecule at a given temperature. It is shown that for molecules of base pairs fewer than than 21, the entire single strand moves in the direction of applied force, whereas for molecules having base pairs more than 21, part of the strand moves in the opposite direction under the influence of force acting on the other strand. This result as well as the calculated values of F(c) as a function of length of dsDNA molecules are in very good agreement with the experimental values of Hatch et al. [Phys. Rev. E 78, 011920 (2008)].

Petra Schwille - One of the best experts on this subject based on the ideXlab platform.

  • Diffusion and Segmental Dynamics of Double-Stranded DNA
    Physical Review Letters, 2006
    Co-Authors: Eugene P. Petrov, Thomas Ohrt, Roland G. Winkler, Petra Schwille
    Abstract:

    (Received 28 January 2006; published 18 December 2006)Diffusion and segmental dynamics of the Double-Stranded -phage DNA polymer are quantitativelystudied over the transition range from stiff to semiflexible chains. Spectroscopy of fluorescence fluctua-tions of single-end fluorescently labeled monodisperse DNA fragments unambiguously shows that Double-Stranded DNA in the length range of 10

  • Diffusion and Segmental Dynamics of Double-Stranded DNA
    Physical review letters, 2006
    Co-Authors: Eugene P. Petrov, Thomas Ohrt, Roland G. Winkler, Petra Schwille
    Abstract:

    Diffusion and segmental dynamics of the Double-Stranded lambda-phage DNA polymer are quantitatively studied over the transition range from stiff to semiflexible chains. Spectroscopy of fluorescence fluctuations of single-end fluorescently labeled monodisperse DNA fragments unambiguously shows that Double-Stranded DNA in the length range of 10(2) - 2 x 10(4) base pairs behaves as a semiflexible polymer with segmental dynamics controlled by hydrodynamic interactions.