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Science 20 November 1992:
Vol. 258. no. 5086, pp. 1320 - 1324
DOI: 10.1126/science.1280856
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Articles

Science, Vol 258, Issue 5086, 1320-1324
Copyright © 1992 by American Association for the Advancement of Science

articles

Functional transcription elongation complexes from synthetic RNA-DNA bubble duplexes

SS Daube and PH von Hippel

Institute of Molecular Biology, University of Oregon, Eugene 97403.

A synthetic RNA-DNA bubble duplex construct intended to mimic the nucleic acid framework of a functional transcription elongation complex was designed and assembled. The construct consisted of a double-stranded DNA duplex of variable length (the template and nontemplate strands) containing an internal noncomplementary DNA "bubble" sequence. The 3' end of an RNA oligonucleotide that is partially complementary to the template DNA strand was hybridized within the DNA bubble to form an RNA-DNA duplex with a non-complementary 5'-terminal RNA tail. The addition of either Escherichia coli or T7 RNA polymerase to this construct formed a complex that synthesized RNA with good efficiency from the hybridized RNA primer in a template-directed and processive manner, and displayed other features of a normal promoter-initiated transcription elongation complex. Other such constructs can be designed to examine many of the functional and regulatory properties of transcription systems.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Direct Spectroscopic Study of Reconstituted Transcription Complexes Reveals That Intrinsic Termination Is Driven Primarily by Thermodynamic Destabilization of the Nucleic Acid Framework.
K. Datta and P. H. von Hippel (2008)
J. Biol. Chem. 283, 3537-3549
   Abstract »    Full Text »    PDF »
Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement.
S. Naji, M. G. Bertero, P. Spitalny, P. Cramer, and M. Thomm (2008)
Nucleic Acids Res. 36, 676-687
   Abstract »    Full Text »    PDF »
Direct Versus Limited-step Reconstitution Reveals Key Features of an RNA Hairpin-stabilized Paused Transcription Complex.
S. Kyzer, K. S. Ha, R. Landick, and M. Palangat (2007)
J. Biol. Chem. 282, 19020-19028
   Abstract »    Full Text »    PDF »
Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase.
V. S. Anand and S. S. Patel (2006)
J. Biol. Chem. 281, 35677-35685
   Abstract »    Full Text »    PDF »
Initial Bubble Collapse Plays a Key Role in the Transition to Elongation in T7 RNA Polymerase.
P. Gong, E. A. Esposito, and C. T. Martin (2004)
J. Biol. Chem. 279, 44277-44285
   Abstract »    Full Text »    PDF »
Characterization of T7 RNA Polymerase Transcription Complexes Assembled on Nucleic Acid Scaffolds.
D. Temiakov, M. Anikin, and W. T. McAllister (2002)
J. Biol. Chem. 277, 47035-47043
   Abstract »    Full Text »    PDF »
Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase.
Y. W. Yin and T. A. Steitz (2002)
Science 298, 1387-1395
   Abstract »    Full Text »    PDF »
A Structural Model of Transcription Elongation.
N. Korzheva, A. Mustaev, M. Kozlov, A. Malhotra, V. Nikiforov, A. Goldfarb, and S. A. Darst (2000)
Science 289, 619-625
   Abstract »    Full Text »
The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex.
M. L. Kireeva, N. Komissarova, D. S. Waugh, and M. Kashlev (2000)
J. Biol. Chem. 275, 6530-6536
   Abstract »    Full Text »    PDF »
Interactions of Escherichia coli sigma 70 within the transcription elongation complex.
S. S. Daube and P. H. von Hippel (1999)
PNAS 96, 8390-8395
   Abstract »    Full Text »    PDF »
The recombination hotspot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5'-GCTGGTGG-3'.
P. R. Bianco and S. C. Kowalczykowski (1997)
PNAS 94, 6706-6711
   Abstract »    Full Text »    PDF »
A novel 3'-end repair mechanism in an RNA virus.
P. D. Nagy, C. D. Carpenter, and A. E. Simon (1997)
PNAS 94, 1113-1118
   Abstract »    Full Text »    PDF »
Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS.
C. Jeon and K. Agarwal (1996)
PNAS 93, 13677-13682
   Abstract »    Full Text »    PDF »
The Binding of UvrAB Proteins to Bubble and Loop Regions in Duplex DNA.
B. Ahn and L. Grossman (1996)
J. Biol. Chem. 271, 21462-21470
   Abstract »    Full Text »    PDF »
Accelerated Hybridization of Oligonucleotides to Duplex DNA.
M. Iyer, J. C. Norton, and D. R. Corey (1995)
J. Biol. Chem. 270, 14712-14717
   Abstract »    Full Text »    PDF »
Structure and Function of Transcription-Repair Coupling Factor.
C. P. Selby and A. Sancar (1995)
J. Biol. Chem. 270, 4882-4889
   Abstract »    Full Text »    PDF »
Structure and Function of Transcription-Repair Coupling Factor.
C. P. Selby and A. Sancar (1995)
J. Biol. Chem. 270, 4890-4895
   Abstract »    Full Text »    PDF »
Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 A Resolution.
A. L. Gnatt, P. Cramer, J. Fu, D. A. Bushnell, and R. D. Kornberg (2001)
Science 292, 1876-1882
   Abstract »    Full Text »    PDF »
Efficient bacterial transcription of DNA nanocircle vectors with optimized single-stranded promoters.
T. Ohmichi, A. Maki, and E. T. Kool (2002)
PNAS 99, 54-59
   Abstract »    Full Text »    PDF »


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