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J. Biol. Chem., Vol. 281, Issue 34, 24441-24448, August 25, 2006

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Observed Instability of T7 RNA Polymerase Elongation Complexes Can Be Dominated by Collision-induced "Bumping"^*

Yi Zhou¹ and Craig T. Martin^¶2

From the Program in Molecular and Cellular Biology, Department of Biochemistry and Molecular Biology, and ^¶Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003

T7 RNA polymerase elongates RNA at a relatively high rate and can displace many tightly bound protein-DNA complexes. Despite these properties, measurements of the stability of stalled elongation complexes have shown lifetimes that are much shorter than those of the multisubunit RNA polymerases. In this work, we demonstrate that the apparent instability of stalled complexes actually arises from the action of trailing RNA polymerases (traveling in the same direction) displacing the stalled complex. Moreover, the instability caused by collision between two polymerases is position dependent. A second polymerase is blocked from promoter binding when a leading complex is stalled 12 bp or less from the promoter. The trailing complex can bind and make abortive transcripts when the leading complex is between 12 and 20 bp from the promoter, but it cannot displace the first complex since it is in a unstable initiation conformation. Only when the leading complex is stalled more than 20 bp away from the promoter can a second polymerase bind, initiate, and displace the leading complex.

Received for publication, May 8, 2006 , and in revised form, June 28, 2006.

^* This work was supported in part by National Institutes of Health Grant 1RO1 GM55002. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ Supported by National Research Service Award T32 GM08515 from the National Institutes of Health.

² To whom correspondence should be addressed: Dept. of Chemistry, University of Massachusetts Amherst, 701 LGRC, 710 North Pleasant St., Amherst, MA 01003-9336. Tel.: 413-545-3299; Fax: 413-545-4490; E-mail: cmartin{at}chem.umass.edu.

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This article has been cited by other articles:

				Y. Zhou, D. M. Navaroli, M. S. Enuameh, and C. T. Martin Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism PNAS, June 19, 2007; 104(25): 10352 - 10357. [Abstract] [Full Text] [PDF]