title: Promoter scanning for transcription inhibition with DNA-binding polyamides.
abstract: When targeted to sequences adjacent to a TATA element, pyrrole-imidazole (Py-Im) polyamides inhibit the DNA binding activity of TATA box binding protein (TBP) and basal transcription by RNA polymerase II. In the present study, we scanned the human immunodeficiency virus type 1 promoter for polyamide inhibition of TBP binding and transcription using a series of DNA constructs in which a polyamide binding site was placed at various distances from the TATA box. Polyamide interference with either TBP-DNA or TFIID-TFIIA-DNA contacts both upstream and downstream of the TATA element resulted in inhibition of transcription. Our results define important protein-DNA interactions outside of the TATA element and suggest that transcription inhibition of selected gene promoters can be achieved with polyamides that target unique sequences within these promoters at a distance from the TATA element. Our studies also demonstrate the utility of the Py-Im polyamides for discovery of functionally important protein-DNA contacts involved in transcription.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Ehley
authors.forename: Christian
authors.initials: C
authors.lastname: Melander
authors.forename: David
authors.initials: D
authors.lastname: Herman
authors.forename: Eldon E
authors.initials: EE
authors.lastname: Baird
authors.forename: Heather A
authors.initials: HA
authors.lastname: Ferguson
authors.forename: James A
authors.initials: JA
authors.lastname: Goodrich
authors.forename: Peter B
authors.initials: PB
authors.lastname: Dervan
authors.forename: Joel M
authors.initials: JM
authors.lastname: Gottesfeld
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000187:drug effects / Q000502:physiology; D001667:Binding, Competitive / Q000187:drug effects; D002474:Cell-Free System; D018983:DNA Footprinting; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009757:Nylons / Q000737:chemistry / Q000494:pharmacology*; D011401:Promoter Regions, Genetic / Q000187:drug effects* / Q000235:genetics; D013379:Substrate Specificity / Q000502:physiology; D016385:TATA Box / Q000502:physiology; D035181:TATA-Box Binding Protein; D035561:Transcription Factor TFIIA; D035362:Transcription Factor TFIID; D014157:Transcription Factors / Q000378:metabolism; D019473:Transcription Factors, TFII / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects*
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D009757:Nylons; D035181:TATA-Box Binding Protein; D035561:Transcription Factor TFIIA; D035362:Transcription Factor TFIID; D014157:Transcription Factors; D019473:Transcription Factors, TFII