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Robert Kaptein - One of the best experts on this subject based on the ideXlab platform.

  • Zinc-finger structures
    Current Opinion in Structural Biology, 1992
    Co-Authors: Robert Kaptein
    Abstract:

    Abstract Although the spatial structures of various classes of zinc-finger peptides were known from two-dimensional NMR studies, our knowledge about their interaction with DNA has dramatically increased during the past year. In particular, for the two major classes of zinc fingers, i.e. the transcription factor IIIA-like fingers and those of the nuclear hormone receptors, the structures of protein-DNA complexes have been solved by X-ray crystallography. Thus, we now know how the three-finger DNA-binding domain of the mouse protein Zif268 recognizes its DNA-binding site and, similarly, the Interactions between the glucocorticoid receptor and its hormone response element have been revealed. This work and other zinc-finger studies are reviewed with a special emphasis on the structural aspects of zinc fingers and their Interactions with DNA.

Alan P Wolffe - One of the best experts on this subject based on the ideXlab platform.

  • Asymmetric linker histone association directs the asymmetric rearrangement of core histone Interactions in a positioned nucleosome containing a thyroid hormone response element.
    Biochemistry, 1998
    Co-Authors: Dmitry Guschin, Simon P Chandler, Alan P Wolffe
    Abstract:

    We describe histone-DNA cross-linking in a positioned nucleosome containing a thyroid hormone response element (TRE) from the Xenopus laevis thyroid hormone receptor betaA gene (TRbetaA). Histones H3 and H4 are cross-linked to DNA in the nucleosome core within 30 base pairs to either side of the dyad axis. Histone H2A cross-links to DNA in the core at the dyad axis, and histones H2A and H2B have extensive Interactions with DNA 40-80 bp away from the dyad axis. Linker histone H5 and the globular domain of Xenopus H1(0) associate asymmetrically with DNA at one edge of the TRbetaA nucleosome. Nevertheless, the asymmetric association of H5 leads to a significant rearrangement of core histone-DNA contacts at the dyad axis of the nucleosome. In the presence of linker histone, cross-linkings of H4 within 15 bp to one side of the dyad axis, of histone H2A at the dyad axis, and of H2A and H2B 40-80 bp to one side of the dyad axis are all reduced. This reduction in cross-linking occurs preferentially on the side of the nucleosome to which H5 is bound. Our results indicate that core histone contacts within mononucleosomes are conformationally dynamic and that linker histone incorporation at the edge of the nucleosome can influence core histone-DNA Interactions in an asymmetric way including contacts at the dyad axis.

  • asymmetric linker histone association directs the asymmetric rearrangement of core histone Interactions in a positioned nucleosome containing a thyroid hormone response element
    Biochemistry, 1998
    Co-Authors: Dmitry Guschin, Simon P Chandler, Alan P Wolffe
    Abstract:

    We describe histone−DNA cross-linking in a positioned nucleosome containing a thyroid hormone response element (TRE) from the Xenopus laevis thyroid hormone receptor βA gene (TRβA). Histones H3 and H4 are cross-linked to DNA in the nucleosome core within 30 base pairs to either side of the dyad axis. Histone H2A cross-links to DNA in the core at the dyad axis, and histones H2A and H2B have extensive Interactions with DNA 40−80 bp away from the dyad axis. Linker histone H5 and the globular domain of Xenopus H1° associate asymmetrically with DNA at one edge of the TRβA nucleosome. Nevertheless, the asymmetric association of H5 leads to a significant rearrangement of core histone−DNA contacts at the dyad axis of the nucleosome. In the presence of linker histone, cross-linkings of H4 within 15 bp to one side of the dyad axis, of histone H2A at the dyad axis, and of H2A and H2B 40−80 bp to one side of the dyad axis are all reduced. This reduction in cross-linking occurs preferentially on the side of the nucleo...

James M Berger - One of the best experts on this subject based on the ideXlab platform.

  • the structure of DNA bound human topoisomerase ii alpha conformational mechanisms for coordinating inter subunit Interactions with DNA cleavage
    Journal of Molecular Biology, 2012
    Co-Authors: Timothy J Wendorff, Caroline A Austin, Bryan H Schmidt, Pauline Heslop, James M Berger
    Abstract:

    Type II topoisomerases are required for the management of DNA superhelicity and chromosome segregation, and serve as frontline targets for a variety of small-molecule therapeutics. To better understand how these enzymes act in both contexts, we determined the 2.9‐A‐resolution structure of the DNA cleavage core of human topoisomerase IIα (TOP2A) bound to a doubly nicked, 30‐bp duplex oligonucleotide. In accord with prior biochemical and structural studies, TOP2A significantly bends its DNA substrate using a bipartite, nucleolytic center formed at an N-terminal dimerization interface of the cleavage core. However, the protein also adopts a global conformation in which the second of its two inter-protomer contact points, one at the C-terminus, has separated. This finding, together with comparative structural analyses, reveals that the principal site of DNA engagement undergoes highly quantized conformational transitions between distinct binding, cleavage, and drug-inhibited states that correlate with the control of subunit–subunit Interactions. Additional consideration of our TOP2A model in light of an etoposide-inhibited complex of human topoisomerase IIβ (TOP2B) suggests possible modification points for developing paralog-specific inhibitors to overcome the tendency of topoisomerase II-targeting chemotherapeutics to generate secondary malignancies.

Dmitry Guschin - One of the best experts on this subject based on the ideXlab platform.

  • Asymmetric linker histone association directs the asymmetric rearrangement of core histone Interactions in a positioned nucleosome containing a thyroid hormone response element.
    Biochemistry, 1998
    Co-Authors: Dmitry Guschin, Simon P Chandler, Alan P Wolffe
    Abstract:

    We describe histone-DNA cross-linking in a positioned nucleosome containing a thyroid hormone response element (TRE) from the Xenopus laevis thyroid hormone receptor betaA gene (TRbetaA). Histones H3 and H4 are cross-linked to DNA in the nucleosome core within 30 base pairs to either side of the dyad axis. Histone H2A cross-links to DNA in the core at the dyad axis, and histones H2A and H2B have extensive Interactions with DNA 40-80 bp away from the dyad axis. Linker histone H5 and the globular domain of Xenopus H1(0) associate asymmetrically with DNA at one edge of the TRbetaA nucleosome. Nevertheless, the asymmetric association of H5 leads to a significant rearrangement of core histone-DNA contacts at the dyad axis of the nucleosome. In the presence of linker histone, cross-linkings of H4 within 15 bp to one side of the dyad axis, of histone H2A at the dyad axis, and of H2A and H2B 40-80 bp to one side of the dyad axis are all reduced. This reduction in cross-linking occurs preferentially on the side of the nucleosome to which H5 is bound. Our results indicate that core histone contacts within mononucleosomes are conformationally dynamic and that linker histone incorporation at the edge of the nucleosome can influence core histone-DNA Interactions in an asymmetric way including contacts at the dyad axis.

  • asymmetric linker histone association directs the asymmetric rearrangement of core histone Interactions in a positioned nucleosome containing a thyroid hormone response element
    Biochemistry, 1998
    Co-Authors: Dmitry Guschin, Simon P Chandler, Alan P Wolffe
    Abstract:

    We describe histone−DNA cross-linking in a positioned nucleosome containing a thyroid hormone response element (TRE) from the Xenopus laevis thyroid hormone receptor βA gene (TRβA). Histones H3 and H4 are cross-linked to DNA in the nucleosome core within 30 base pairs to either side of the dyad axis. Histone H2A cross-links to DNA in the core at the dyad axis, and histones H2A and H2B have extensive Interactions with DNA 40−80 bp away from the dyad axis. Linker histone H5 and the globular domain of Xenopus H1° associate asymmetrically with DNA at one edge of the TRβA nucleosome. Nevertheless, the asymmetric association of H5 leads to a significant rearrangement of core histone−DNA contacts at the dyad axis of the nucleosome. In the presence of linker histone, cross-linkings of H4 within 15 bp to one side of the dyad axis, of histone H2A at the dyad axis, and of H2A and H2B 40−80 bp to one side of the dyad axis are all reduced. This reduction in cross-linking occurs preferentially on the side of the nucleo...

M Nethaji - One of the best experts on this subject based on the ideXlab platform.

  • synthesis x ray structure and in vitro cytotoxicity studies of cu i ii complexes of thiosemicarbazone special emphasis on their Interactions with DNA
    Dalton Transactions, 2015
    Co-Authors: Ayon Chakraborty, S Dash, Alok Kumar Panda, Rama Acharyya, Ashis Biswas, Subhadip Mukhopadhyay, Sujit K Bhutia, Aurelien Crochet, Yogesh P Patil, M Nethaji
    Abstract:

    4-(p-X-phenyl)thiosemicarbazone of napthaldehyde {where X = Cl (HL1) and X = Br (HL2)}, thiosemicarbazone of quinoline-2-carbaldehyde (HL3) and 4-(p-fluorophenyl)thiosemicarbazone of salicylaldehyde (H2L4) and their copper(I) {[Cu(HL1)(PPh3)2Br]·CH3CN (1) and [Cu(HL2)(PPh3)2Cl]·DMSO (2)} and copper(II) {[(Cu2L32Cl)2(μ-Cl)2]·2H2O (3) and [Cu(L4)(Py)] (4)} complexes are reported herein. The synthesized ligands and their copper complexes were successfully characterized by elemental analysis, cyclic voltammetry, NMR, ESI-MS, IR and UV-Vis spectroscopy. Molecular structures of all the Cu(I) and Cu(II) complexes have been determined by X-ray crystallography. All the complexes (1–4) were tested for their ability to exhibit DNA-binding and -cleavage activity. The complexes effectively interact with CT-DNA possibly by groove binding mode, with binding constants ranging from 104 to 105 M−1. Among the complexes, 3 shows the highest chemical (60%) as well as photo-induced (80%) DNA cleavage activity against pUC19 DNA. Finally, the in vitro antiproliferative activity of all the complexes was assayed against the HeLa cell line. Some of the complexes have proved to be as active as the clinical referred drugs, and the greater potency of 3 may be correlated with its aqueous solubility and the presence of the quinonoidal group in the thiosemicarbazone ligand coordinated to the metal.