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  • 1
    Publication Date: 1998-07-17
    Description: During RNA synthesis in the ternary elongation complex, RNA polymerase enzyme holds nucleic acids in three contiguous sites: the double-stranded DNA-binding site (DBS) ahead of the transcription bubble, the RNA-DNA heteroduplex-binding site (HBS), and the RNA-binding site (RBS) upstream of HBS. Photochemical cross-linking allowed mapping of the DNA and RNA contacts to specific positions on the amino acid sequence. Unexpectedly, the same protein regions were found to participate in both DBS and RBS. Thus, DNA entry and RNA exit occur close together in the RNA polymerase molecule, suggesting that the three sites constitute a single unit. The results explain how RNA in the integrated unit RBS-HBS-DBS may stabilize the ternary complex, whereas a hairpin in RNA result in its dissociation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Gusarov, I -- Avetissova, E -- Kozlov, M -- Goldfarb, A -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):424-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA. evgeny.nudler@med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665887" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA, Bacterial/chemistry/*metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Escherichia coli/*genetics/metabolism ; Idoxuridine/metabolism ; Models, Genetic ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/*metabolism ; Protein Binding ; RNA, Bacterial/chemistry/*metabolism ; Templates, Genetic ; *Transcription, Genetic ; Ultraviolet Rays
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2000-08-01
    Description: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzheva, N -- Mustaev, A -- Kozlov, M -- Malhotra, A -- Nikiforov, V -- Goldfarb, A -- Darst, S A -- GM30717/GM/NIGMS NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):619-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915625" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 1996-07-12
    Description: The elongation of RNA chains during transcription occurs in a ternary complex containing RNA polymerase (RNAP), DNA template, and nascent RNA. It is shown here that elongating RNAP from Escherichia coli can switch DNA templates by means of end-to-end transposition without loss of the transcript. After the switch, transcription continues on the new template. With the use of defined short DNA fragments as switching templates, RNAP-DNA interactions were dissected into two spatially distinct components, each contributing to the stability of the elongating complex. The front (F) interaction occurs ahead of the growing end of RNA. This interaction is non-ionic and requires 7 to 9 base pairs of intact DNA duplex. The rear (R) interaction is ionic and requires approximately six nucleotides of the template DNA strand behind the active site and one nucleotide ahead of it. The nontemplate strand is not involved. With the use of protein-DNA crosslinking, the F interaction was mapped to the conserved zinc finger motif in the NH2-terminus of the beta' subunit and the R interaction, to the COOH-terminal catalytic domain of the beta subunit. Mutational disruption of the zinc finger selectively destroyed the F interaction and produced a salt-sensitive ternary complex with diminished processivity. A model of the ternary complex is proposed here that suggests that trilateral contacts in the active center maintain the nonprocessive complex, whereas a front-end domain including the zinc finger ensures processivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Avetissova, E -- Markovtsov, V -- Goldfarb, A -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):211-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662499" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA/chemistry/*metabolism ; DNA, Single-Stranded/metabolism ; DNA-Directed RNA Polymerases/chemistry/genetics/*metabolism ; Escherichia coli/enzymology ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Binding ; RNA, Messenger/metabolism ; Sodium Chloride/pharmacology ; Templates, Genetic ; *Transcription, Genetic ; Zinc Fingers/genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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