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Science 17 November 2006:
Vol. 314. no. 5802, pp. 1139 - 1143
DOI: 10.1126/science.1131398
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Reports

Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching

Andrey Revyakin,1,2* Chenyu Liu,1,2,3 Richard H. Ebright,1{dagger} Terence R. Strick2,3{dagger}

Using single-molecule DNA nanomanipulation, we show that abortive initiation involves DNA "scrunching"—in which RNA polymerase (RNAP) remains stationary and unwinds and pulls downstream DNA into itself—and that scrunching requires RNA synthesis and depends on RNA length. We show further that promoter escape involves scrunching, and that scrunching occurs in most or all instances of promoter escape. Our results support the existence of an obligatory stressed intermediate, with approximately one turn of additional DNA unwinding, in escape and are consistent with the proposal that stress in this intermediate provides the driving force to break RNAP-promoter and RNAP-initiation-factor interactions in escape.

1 Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
3 Institut Jacques Monod, Centre National de la Recherche Scientifique UMR 7592 and Universités de Paris VI et Paris VII, 2 Place Jussieu, 75251 Paris Cedex 05, France.

* Present address: Howard Hughes Medical Institute and Department of Molecular and Cell Biology, 16 Barker Hall, University of California, Berkeley, CA 94720–3204, USA.

{dagger} To whom correspondence should be addressed. E-mail: strick{at}ijm.jussieu.fr (T.R.S.); ebright{at}waksman.rutgers.edu (R.H.E.)

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