Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase

Journal of Molecular Biology

Volumn 308, Issue 3, 2001, Pages 465-475

  Liu, Cuihua ^a   Martin, Craig T ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

Base analog; Elongation; Melting; Transcription bubble; Translocation

Indexed keywords

ELONGATION FACTOR; RNA POLYMERASE;

ARTICLE; COMPLEX FORMATION; DNA RNA HYBRIDIZATION; ENZYME ACTIVE SITE; ENZYME STABILITY; FLUORESCENCE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS; TRANSCRIPTION REGULATION;

EID: 0035804928     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4601     Document Type: Article

References (34)

1. Bacteriophage T7 late promoters with point mutations: Quantitative foot-printing and in vivo expression
2. Structure of a transcribing T7 RNA polymerase initiation complex
3. Structural basis for initiation of transcription from an RNA polymerase-promoter complex
4. Cloning and expression of the gene for bacteriophage T7 RNA polymerase
5. Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement
6. A model for the mechanism of polymerase translocation
7. Interactions of T7 RNA polymerase with T7 late promoters measured by footprinting with methidiumpropyl-EDTA-iron(II)
8. Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners
9. T7 RNA polymerase elongation complex structure and movement
10. Interactions of the RNA polymerase of bacteriophage T7 with its promoter during binding and initiation of transcription
11. Interactions of a proteolytically nicked RNA polymerase of bacteriophage T7 with its promoter
12. Equilibrium and stopped-flow kinetic studies of interaction between T7 RNA polymerase and its promoters measured by protein and 2-aminopurine fluorescence changes
13. Transcription by T7 RNA polymerase is not zinc-dependent and is abolished on amidomethylation of cysteine-347
14. Major groove recognition elements in the middle of the T7 RNA polymerase promoter
15. Structure and function of the bacteriophage T7 RNA polymerase (or, the virtues of simplicity)
16. Characterization of halted T7 RNA polymerase elongation complexes reveals multiple factors that contribute to stability
17. Structural analysis of ternary complexes of Escherichia coli RNA polymerase: Ribonuclease footprinting of the nascent RNA in complexes
18. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase
19. Spatial organization of transcription elongation complex in Escherichia coli
20. T7 ribonucleic acid polymerase-promoter interactions
21. Promoter specificity determinants of T7 RNA polymerase
22. The influence of RNA and DNA template structures during transcript elongation by RNA polymerases
23. A direct real-time spectroscopic investigation of the mechanism of open complex formation by T7 RNA polymerase
24. Identification of specific contacts in T3 RNA polymerase-promoter interactions: Kinetic analysis using small synthetic promoters
25. Structural and mechanistic relationships between nucleic acid polymerases
26. Spectroscopic determination of open complex formation at promoters for Escherichia coli RNA polymerase
27. The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance
28. RNA folding during transcription by T7 RNA polymerase analyzed using the self-cleaving transcript assay
29. Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase
30. Basic mechanisms of transcript elongation and its regulation
31. Positioning of the start site in the initiation of transcription by bacteriophage T7 RNA polymerase
32. Determinants of the stability of transcription elongation complexes: Interactions of the nascent RNA with the DNA template and the RNA polymerase
33. Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption
34. Sequence dependence of energy transfer in DNA oligonucleotides