title: Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release.
abstract: BACKGROUND
  The sequence-specific, hairpin-independent termination signal for the bacteriophage RNA polymerases in Escherichia coli rrnB t1 terminator consists of two modules. The upstream module includes the conserved sequence and the downstream one is U-rich.
  
  
  RESULTS
  Elongation complexes of T7 RNA polymerase paused 2 bp before reaching the termination site at a 500 microM concentration of NTP. At 5-50 microM NTP, however, they paused and terminated there or resumed elongation beyond the termination site. Only at higher concentrations of NTP (500 microM), the pause complex proceeded slowly to and became incompetent at the termination site. At 4 bp or more before the termination site, the unprotected single-stranded region of transcription bubble shrank at the trailing edge to 4-5 bp from approximately 10 bp, resulting from duplex formation of the conserved sequence. The pause and bubble collapse were not observed with an inactive mutant of the termination signal.
  
  
  CONCLUSIONS
  Sequence-specific termination requires the slow elongation mode of paused conformation, working only at high concentrations of NTP for a few bp prior to the RNA release site. The collapse of bubble that was observed several base pairs before the termination site and/or the resulting duplex might subsequently lead to the paused conformation of T7 elongation complexes.
authors.affiliation: Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Kusong-dong, Yusong-gu, Taejon 305-701.
authors.forename: H
authors.initials: H
authors.lastname: Song
authors.forename: C
authors.initials: C
authors.lastname: Kang
mesh_terms: D017123:Bacteriophage T7 / Q000201:enzymology* / Q000235:genetics; D001483:Base Sequence; D017931:DNA Primers / Q000737:chemistry; D004274:DNA, Recombinant / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D008969:Molecular Sequence Data; D010957:Plasmids; D011487:Protein Conformation; D012329:RNA, Bacterial / Q000378:metabolism*; D014158:Transcription, Genetic; D014764:Viral Proteins
chemical_list: D017931:DNA Primers; D004274:DNA, Recombinant; D012329:RNA, Bacterial; D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases