title: RNA displacement and resolution of the transcription bubble during transcription by T7 RNA polymerase.
abstract: Unlike DNA polymerases, RNA polymerases (RNAPs) must displace the nascent product from the template and restore the DNA to duplex form after passage of the transcription complex. To accomplish this, RNAPs establish a locally denatured "bubble" that encloses a short RNA:DNA hybrid. As the polymerase advances along the template, the RNA is displaced at the trailing edge of the bubble and the two DNA strands are reannealed. Structural analyses have revealed a number of elements that are likely to be involved in this process in T7 RNAP. In this work, we used genetic and biochemical methods to explore the roles of these elements during the transition from an initiation complex to an elongation complex. The results indicate that the transition is a multistep process and reveal a critical role for the nontemplate strand of the DNA.
authors.affiliation: Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, NY 11203, USA.
authors.forename: Manli
authors.initials: M
authors.lastname: Jiang
authors.forename: Na
authors.initials: N
authors.lastname: Ma
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: William T
authors.initials: WT
authors.lastname: McAllister
mesh_terms: D001483:Base Sequence / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000096:biosynthesis* / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D005809:Genes, Regulator / Q000235:genetics; D008958:Models, Molecular; D015394:Molecular Structure; D009711:Nucleotides / Q000235:genetics; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013698:Templates, Genetic; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*; D014764:Viral Proteins
chemical_list: D009711:Nucleotides; D014764:Viral Proteins; D012313:RNA; D004247:DNA; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases