Promoter Scanning for Transcription Inhibition with DNA-Binding Polyamides

REFERENCES

• Baird, E. E., and P. B. Dervan. 1996. Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am. Chem. Soc. 118: 6141–6146.
   Web of Science ®Google Scholar
• Chi, T., and M. Carey. 1996. Assembly of the isomerized TFIIA-TFIID-TATA ternary complex is necessary and sufficient for gene activation. Genes Dev. 10: 2540–2550.
   PubMedGoogle Scholar
• Coulombe, B., and Z. F. Burton. 1999. DNA bending and wrapping around RNA polymerase: a “revolutionary” model describing transcriptional mechanisms. Microbiol. Mol. Biol. Rev. 63: 457–478.
   PubMed Web of Science ®Google Scholar
• Coulombe, B., J. Li, and J. Greenblatt. 1994. Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter. J. Biol. Chem. 269: 19962–19967.
   PubMedGoogle Scholar
• Cox, J. M., M. M. Hayward, J. F. Sanchez, L. D. Gegnas, S. van der Zee, J. H. Dennis, P. B. Sigler, and A. Schepartz. 1997. Bidirectional binding of the TATA box binding protein to the TATA box. Proc. Natl. Acad. Sci. USA 94: 13475–13480.
   PubMedGoogle Scholar
• Dervan, P. B., and R. W. Burli. 1999. Sequence-specific DNA recognition by polyamides. Curr. Opin. Chem. Biol. 3: 688–693.
   PubMed Web of Science ®Google Scholar
• Dickinson, L. A., R. J. Gulizia, J. W. Trauger, E. E. Baird, D. E. Mosier, J. M. Gottesfeld, and P. B. Dervan. 1998. Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands. Proc. Natl. Acad. Sci. USA 95: 12890–12895.
   PubMed Web of Science ®Google Scholar
• Dickinson, L. A., J. W. Trauger, E. E. Baird, P. B. Dervan, B. J. Graves, and J. M. Gottesfeld. 1999. Inhibition of Ets-1 DNA binding and ternary complex formation between Ets-1, NF-kB, and DNA by a designed DNA-binding ligand. J. Biol. Chem. 274: 12765–12773.
   PubMedGoogle Scholar
• Dickinson, L. A., J. W. Trauger, E. E. Baird, P. Ghazal, P. B. Dervan, and J. M. Gottesfeld. 1999. Anti-repression of RNA polymerase II transcription by pyrrole-imidazole polyamides. Biochemistry 38: 10801–10807.
   PubMed Web of Science ®Google Scholar
• Dignam, J. D., P. L. Martin, B. S. Shastry, and R. G. Roeder. 1983. Eucaryotic gene transcription with purified components. Methods Enzymol. 101: 582–598.
   PubMed Web of Science ®Google Scholar
• Galasinski, S. K., T. N. Lively, A. De Barron, and J. A. Goodrich. 2000. Acetyl coenzyme A stimulates RNA polymerase II transcription and promoter binding by transcription factor IID in the absence of histones. Mol. Cell. Biol. 20: 1923–1930.
   PubMedGoogle Scholar
• Geiger, J. H., S. Hahn, S. Lee, and P. B. Sigler. 1996. Crystal structure of the yeast TFIIA/TBP/DNA complex. Science 272: 830–836.
   PubMed Web of Science ®Google Scholar
• Gottesfeld, J. M., J. M. Turner, and P. B. Dervan. 2000. Chemical approaches to control gene expression. Gene Expr. 9: 77–91.
   PubMed Web of Science ®Google Scholar
• Grove, A., A. Galeone, E. Yu, L. Mayol, and E. P. Geiduschek. 1998. Affinity, stability and polarity of binding of the TATA binding protein governed by flexure at the TATA box. J. Mol. Biol. 282: 731–739.
   PubMed Web of Science ®Google Scholar
• Harrich, D., J. Garcia, F. Wu, R. Mitsuyasu, J. Gonazalez, and R. Gaynor. 1989. Role of SP1-binding domains in in vivo transcriptional regulation of the human immunodeficiency virus type 1 long terminal repeat. J. Virol. 63: 2585–2591.
   PubMedGoogle Scholar
• Hernandez, N. 1993. TBP, a universal eukaryotic transcription factor? Genes Dev. 7: 1291–1308.
   PubMed Web of Science ®Google Scholar
• Janssen, S., O. Cuvier, M. Müller, and U. K. Laemmli. 2000. Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster. Mol. Cell 6: 1013–1024.
   PubMed Web of Science ®Google Scholar
• Janssen, S., T. Durussel, and U. K. Laemmli. 2000. Chromatin opening of DNA satellites by targeted sequence-specific drugs. Mol. Cell 6: 999–1011.
   PubMed Web of Science ®Google Scholar
• Jones, K. A., P. A. Luciw, and N. Duchange. 1988. Structural arrangements of transcription control domains within the 5′-untranslated leader regions of the HIV-1 and HIV-2 promoters. Genes Dev. 2: 1101–1114.
   PubMed Web of Science ®Google Scholar
• Jones, K. A., and B. M. Peterlin. 1994. Control of RNA initiation and elongation at the HIV-1 promoter. Annu. Rev. Biochem. 63: 717–743.
   PubMed Web of Science ®Google Scholar
• Juo, Z. S., T. K. Chiu, P. M. Leiberman, I. Baikalov, A. J. Berk, and R. E. Dickerson. 1996. How proteins recognize the TATA box. J. Mol. Biol. 261: 239–254.
   PubMed Web of Science ®Google Scholar
• Kashanchi, F., R. Shibata, E. K. Ross, J. N. Brady, and M. A. Martin. 1994. Second-site long terminal repeat (LTR) revertants of replication-defective human immunodeficiency virus: effects of revertant TATA box motifs on virus infectivity, LTR-directed expression, in vitro RNA synthesis, and binding of basal transcription factors TFIID and TFIIA. J. Virol. 68: 3298–3307.
   PubMed Web of Science ®Google Scholar
• Kielkopf, C. L., E. E. Baird, P. B. Dervan, and D. C. Rees. 1998. Structural basis for GC recognition in the DNA minor groove. Nature Struct. Biol. 5: 104–109.
   PubMedGoogle Scholar
• Kim, J. L., D. B. Nikolov, and S. K. Burley. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365: 520–527.
   PubMed Web of Science ®Google Scholar
• Kim, Y., J. H. Geiger, S. Hahn, and P. B. Sigler. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365: 512–520.
   PubMed Web of Science ®Google Scholar
• Lagrange, T., A. N. Kapanidis, H. Tang, D. Reinberg, and R. H. Ebright. 1998. New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12: 34–44.
   PubMed Web of Science ®Google Scholar
• Lagrange, T., T.-K. Kim, G. Orphanides, Y. W. Ebright, R. H. Ebright, and D. Reinberg. 1996. High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex. Proc. Natl. Acad. Sci. USA 93: 10620–10625.
   PubMedGoogle Scholar
• Lemon, B., and R. Tjian. 2000. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14: 2551–2569.
   PubMed Web of Science ®Google Scholar
• Lenzmeier, B. A., E. E. Baird, P. B. Dervan, and J. K. Nyborg. 1999. The Tax protein-DNA interaction is essential for HTLV-I transactivation in vitro. J. Mol. Biol. 291: 731–744.
   PubMedGoogle Scholar
• Long, J. J., A. Leresche, R. W. Kriwacki, and J. M. Gottesfeld. 1998. Repression of TFIIH transcriptional activity and TFIIH-associated cdk7 kinase activity at mitosis. Mol. Cell. Biol. 18: 1467–1476.
   PubMedGoogle Scholar
• Mapp, A. K., A. Z. Ansari, M. Ptashne, and P. B. Dervan. 2000. Activation of gene expression by small molecule transcription factors. Proc. Natl. Acad. Sci. USA 97: 3930–3935.
   PubMed Web of Science ®Google Scholar
• McBryant, S. J., E. E. Baird, J. W. Trauger, P. B. Dervan, and J. M. Gottesfeld. 1999. Minor groove DNA-protein contacts upstream of a tRNA gene detected with a synthetic DNA binding ligand. J. Mol. Biol. 286: 973–981.
   PubMedGoogle Scholar
• Orphanides, G., T. Lagrange, and D. Reinberg. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10: 2657–2683.
   PubMed Web of Science ®Google Scholar
• Robert, F., D. Forget, J. Li, J. Greenblatt, and B. Coulombe. 1996. Localization of subunits of transcription factors IIE and IIF immediately upstream of the transcriptional initiation site of the adenovirus major late promoter. J. Biol. Chem. 271: 8517–8520.
   PubMedGoogle Scholar
• Sheridan, P. L., C. T. Sheline, K. Cannon, M. L. Voz, M. J. Pazin, J. T. Kadonaga, and K. A. Jones. 1995. Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. Genes Dev. 9: 2090–2104.
   PubMed Web of Science ®Google Scholar
• Sun, D., and L. H. Hurley. 1995. TBP binding to the TATA box induces a specific downstream unwinding site that is targeted by pluramycin. Chem. Biol. 2: 457–469.
   PubMedGoogle Scholar
• Sun, X., D. Ma, M. Sheldon, K. Yeung, and D. Reinberg. 1994. Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription. Genes Dev. 8: 2336–2348.
   PubMedGoogle Scholar
• Tan, S., Y. Hunziker, D. F. Sargent, and T. J. Richmond. 1996. Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 381: 127–134.
   PubMed Web of Science ®Google Scholar
• Tan, S., and T. J. Richmond. 1998. Eukaryotic transcription factors. Curr. Opin. Struct. Biol. 8: 41–48.
   PubMedGoogle Scholar
• Trauger, J. W., E. E. Baird, and P. B. Dervan. 1996. Subnanomolar sequence-specific recognition in the minor groove of DNA by designed ligands. Nature (London) 382: 559–561.
   PubMed Web of Science ®Google Scholar
• Tsai, F. T. F., and P. B. Sigler. 2000. Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J. 19: 25–36.
   PubMedGoogle Scholar
• Turner, J. M., S. E. Swalley, E. E. Baird, and P. B. Dervan. 1998. Aliphatic/aromatic amino acid pairings for polyamide recognition in the minor groove of DNA. J. Am. Chem. Soc. 120: 6219–6226.
   Web of Science ®Google Scholar
• White, S., E. E. Baird, and P. B. Dervan. 1997. On the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides. Chem. Biol. 4: 569–578.
   PubMedGoogle Scholar
• White, S., J. W. Szewczyk, J. M. Turner, E. E. Baird, and P. B. Dervan. 1998. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature (London) 391: 468–471.
   PubMed Web of Science ®Google Scholar
• Zenzie-Gregory, B., P. Sheridan, K. A. Jones, and S. T. Smale. 1993. HIV-1 core promoter lacks a simple initiator element but contains a bipartite activator at the transcription start site. J. Biol. Chem. 268: 15823–15832.
   PubMedGoogle Scholar