title: Supercoil-induced extrusion of a regulatory DNA hairpin.
abstract: Bacteriophage N4 virion RNA polymerase (N4 vRNAP) promoters contain inverted repeats, which form a 5- to 7-base-pair stem, 3-base loop hairpin that is required for vRNAP recognition. We show that, contrary to certain theoretical predictions, hairpin extrusion can occur at physiological superhelical densities in a Mg2+-dependent manner. Specific sequences on the template strand are required for hairpin extrusion. These sequences define stable DNA hairpins that are relatively unreactive to single strand-specific probes. In addition, a specific stable hairpin-inducing sequence can regulate transcription in vivo. Thus, a DNA structure, in its natural environment, is involved in transcriptional regulation.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA.
authors.forename: X
authors.initials: X
authors.lastname: Dai
authors.forename: M B
authors.initials: MB
authors.lastname: Greizerstein
authors.forename: K
authors.initials: K
authors.lastname: Nadas-Chinni
authors.forename: L B
authors.initials: LB
authors.lastname: Rothman-Denes
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D017931:DNA Primers; D004278:DNA, Superhelical / Q000737:chemistry* / Q000187:drug effects; D004279:DNA, Viral / Q000737:chemistry* / Q000187:drug effects; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D015967:Gene Expression Regulation, Viral; D008274:Magnesium / Q000494:pharmacology; D016297:Mutagenesis, Site-Directed; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000302:isolation & purification; D017902:Podoviridae / Q000201:enzymology / Q000235:genetics; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D014158:Transcription, Genetic; D014771:Virion / Q000201:enzymology / Q000235:genetics
chemical_list: D017931:DNA Primers; D004278:DNA, Superhelical; D004279:DNA, Viral; D009838:Oligodeoxyribonucleotides; D012321:DNA-Directed RNA Polymerases; D008274:Magnesium