The Experts below are selected from a list of 57 Experts worldwide ranked by ideXlab platform

V A Ivanov - One of the best experts on this subject based on the ideXlab platform.

  • elucidating the DNA Histone Interaction in nucleosome from the DNA dendrimer complex
    Macromolecules, 2016
    Co-Authors: Yenchih Huang, Chunjen Su, Chunyu Chen, Hsinlung Chen, User Jeng, Nikolay V Berezhnoy, Lars Nordenskiold, V A Ivanov
    Abstract:

    The electrostatic complex of DNA with poly(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic Interaction can lead to the key structural features of nucleosome. Both dendrimer and Histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA–HO Interaction is beyond electrostatics, as additional specific Interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

  • Elucidating the DNA–Histone Interaction in Nucleosome from the DNA–Dendrimer Complex
    Macromolecules, 2016
    Co-Authors: Yenchih Huang, Chunjen Su, Chunyu Chen, Hsinlung Chen, User Jeng, Nikolay V Berezhnoy, Lars Nordenskiold, V A Ivanov
    Abstract:

    The electrostatic complex of DNA with poly(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic Interaction can lead to the key structural features of nucleosome. Both dendrimer and Histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA–HO Interaction is beyond electrostatics, as additional specific Interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

  • Beads-on-String Structure of the Electrostatic Complex of DNA with a High-Generation PAMAM Dendrimer
    Journal of Physics: Conference Series, 2011
    Co-Authors: Chunjen Su, Chunyu Chen, Hsinlung Chen, V A Ivanov
    Abstract:

    The electrostatic complexes of polyanionic DNA with cationic dendrimer have been considered as a potential non-viral vector for gene delivery and a model system for understanding DNA-Histone Interaction. Although it is believed that the gene transfection efficiency may be influenced by the structure of the complex, the supramolecular structure of DNA-dendirmer complexes and its dependence on various system parameters such as dendrimer generation number, charge density, charge ratio and ionic strength are not well resolved. In this study, we investigate the structure of the complex of DNA with polyamidoamine (PAMAM) dendrimer of generation nine (G9) by means of synchrotron small angle X-ray scattering (SAXS). It is found that DNA is always able to wrap around the dendrimer to yield the beads-on-string structure irrespective of the charge density of the dendrimer. The effect of charge density on the persistence length of the chromatin-like fiber thus formed and the pitch length of the DNA superheix wrapping around the dendrimer are elucidated from the calculation of the SAXS profiles based on beads-on-string structure models. The first section in your paper

Zbigniew Darzynkiewicz - One of the best experts on this subject based on the ideXlab platform.

  • please do not disturb destruction of chromatin structure by supravital nucleic acid probes revealed by a novel assay of DNA Histone Interaction
    Cytometry Part A, 2008
    Co-Authors: Donald Wlodkowic, Zbigniew Darzynkiewicz
    Abstract:

    The biomarkers designed to be used supravitally are expected to have minimal effect on structure and function of the cell. Unfortunately nearly all fluorochromes developed to probe live cells interact in undesired way with cellular constituents and affect functional pathways. Herein we comment on potential applications of diverse DNA binding probes in view of the recent article by Wojcik & Dobrucki on DRAQ 5 and SYTO 17. The approach used by these authors to assess DNA-Histone Interactions using the cells having Histones tagged with fluorescent proteins offers a valuable tool to study mechanism of action of antitumor drugs targeting DNA. While the effect of many intercalating drugs may be similar to that of DRAQ5, it may be of particular interest to observe the effects induced by intra-strand and inter-strand DNA crosslinking drugs, alkylating agents, Histone deacetylase inhibitors or even anti-metabolites. The cells having Histones tagged with fluorescent proteins thus may serve as biomarkers to probe mechanism of action of drugs targeting DNA or affecting chromatin structure. In fact, because such gross chromatin changes as revealed by dissociation and segregation of Histones from DNA are most likely incompatible with long-term cell survival, the methodology may be applied for rapid screening of investigational antitumor agents.

Donald Wlodkowic - One of the best experts on this subject based on the ideXlab platform.

  • please do not disturb destruction of chromatin structure by supravital nucleic acid probes revealed by a novel assay of DNA Histone Interaction
    Cytometry Part A, 2008
    Co-Authors: Donald Wlodkowic, Zbigniew Darzynkiewicz
    Abstract:

    The biomarkers designed to be used supravitally are expected to have minimal effect on structure and function of the cell. Unfortunately nearly all fluorochromes developed to probe live cells interact in undesired way with cellular constituents and affect functional pathways. Herein we comment on potential applications of diverse DNA binding probes in view of the recent article by Wojcik & Dobrucki on DRAQ 5 and SYTO 17. The approach used by these authors to assess DNA-Histone Interactions using the cells having Histones tagged with fluorescent proteins offers a valuable tool to study mechanism of action of antitumor drugs targeting DNA. While the effect of many intercalating drugs may be similar to that of DRAQ5, it may be of particular interest to observe the effects induced by intra-strand and inter-strand DNA crosslinking drugs, alkylating agents, Histone deacetylase inhibitors or even anti-metabolites. The cells having Histones tagged with fluorescent proteins thus may serve as biomarkers to probe mechanism of action of drugs targeting DNA or affecting chromatin structure. In fact, because such gross chromatin changes as revealed by dissociation and segregation of Histones from DNA are most likely incompatible with long-term cell survival, the methodology may be applied for rapid screening of investigational antitumor agents.

Yenchih Huang - One of the best experts on this subject based on the ideXlab platform.

  • elucidating the DNA Histone Interaction in nucleosome from the DNA dendrimer complex
    Macromolecules, 2016
    Co-Authors: Yenchih Huang, Chunjen Su, Chunyu Chen, Hsinlung Chen, User Jeng, Nikolay V Berezhnoy, Lars Nordenskiold, V A Ivanov
    Abstract:

    The electrostatic complex of DNA with poly(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic Interaction can lead to the key structural features of nucleosome. Both dendrimer and Histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA–HO Interaction is beyond electrostatics, as additional specific Interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

  • Elucidating the DNA–Histone Interaction in Nucleosome from the DNA–Dendrimer Complex
    Macromolecules, 2016
    Co-Authors: Yenchih Huang, Chunjen Su, Chunyu Chen, Hsinlung Chen, User Jeng, Nikolay V Berezhnoy, Lars Nordenskiold, V A Ivanov
    Abstract:

    The electrostatic complex of DNA with poly(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic Interaction can lead to the key structural features of nucleosome. Both dendrimer and Histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA–HO Interaction is beyond electrostatics, as additional specific Interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

Chunjen Su - One of the best experts on this subject based on the ideXlab platform.

  • elucidating the DNA Histone Interaction in nucleosome from the DNA dendrimer complex
    Macromolecules, 2016
    Co-Authors: Yenchih Huang, Chunjen Su, Chunyu Chen, Hsinlung Chen, User Jeng, Nikolay V Berezhnoy, Lars Nordenskiold, V A Ivanov
    Abstract:

    The electrostatic complex of DNA with poly(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic Interaction can lead to the key structural features of nucleosome. Both dendrimer and Histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA–HO Interaction is beyond electrostatics, as additional specific Interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

  • Elucidating the DNA–Histone Interaction in Nucleosome from the DNA–Dendrimer Complex
    Macromolecules, 2016
    Co-Authors: Yenchih Huang, Chunjen Su, Chunyu Chen, Hsinlung Chen, User Jeng, Nikolay V Berezhnoy, Lars Nordenskiold, V A Ivanov
    Abstract:

    The electrostatic complex of DNA with poly(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic Interaction can lead to the key structural features of nucleosome. Both dendrimer and Histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA–HO Interaction is beyond electrostatics, as additional specific Interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

  • Nucleosome-like Structure from Dendrimer-Induced DNA Compaction
    Macromolecules, 2012
    Co-Authors: Chunjen Su, Chunyu Chen, Hsinlung Chen, Hiroki Iwase, Satoshi Koizumi, Takeji Hashimoto
    Abstract:

    Genomic DNA in eukaryotes wraps around Histone proteins to package into the limited space of cell nucleus. Since the precise structure of chromatin is not known in detail, attempts have been made to understand DNA–Histone Interaction and the associated self-organization behavior using synthetic model systems. Using small-angle X-ray and neutron scattering, here we show that the electrostatic attraction between DNA and polyamidoamine (PAMAM) dendrimer of generation nine (G9) led to the formation of beads-on-string structure, where DNA wrapped around the dendrimer tightly to yield the “chromatin-like fiber” composing of the interconnected “nucleosome-like particles”. A “stiff chromatin-like fiber model” and a “wormlike chromatin-like fiber model” were introduced to obtain the theoretical scattering patterns closely resembling the experimentally observed ones, from which the pitch length (P) of the DNA superhelix wrapping around the dendrimer and the interparticle distance (d) of the nucleosome-like particle...

  • Beads-on-String Structure of the Electrostatic Complex of DNA with a High-Generation PAMAM Dendrimer
    Journal of Physics: Conference Series, 2011
    Co-Authors: Chunjen Su, Chunyu Chen, Hsinlung Chen, V A Ivanov
    Abstract:

    The electrostatic complexes of polyanionic DNA with cationic dendrimer have been considered as a potential non-viral vector for gene delivery and a model system for understanding DNA-Histone Interaction. Although it is believed that the gene transfection efficiency may be influenced by the structure of the complex, the supramolecular structure of DNA-dendirmer complexes and its dependence on various system parameters such as dendrimer generation number, charge density, charge ratio and ionic strength are not well resolved. In this study, we investigate the structure of the complex of DNA with polyamidoamine (PAMAM) dendrimer of generation nine (G9) by means of synchrotron small angle X-ray scattering (SAXS). It is found that DNA is always able to wrap around the dendrimer to yield the beads-on-string structure irrespective of the charge density of the dendrimer. The effect of charge density on the persistence length of the chromatin-like fiber thus formed and the pitch length of the DNA superheix wrapping around the dendrimer are elucidated from the calculation of the SAXS profiles based on beads-on-string structure models. The first section in your paper