Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation

doi:10.1073/pnas.0307241101

Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation

^*Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway NJ 08854; and ^†Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724

Edited by Jeffrey W. Roberts, Cornell University, Ithaca, NY, and approved January 28, 2004 (received for review November 6, 2003)

Abstract

By monitoring the end-to-end extension of a mechanically stretched, supercoiled, single DNA molecule, we have been able directly to observe the change in extension associated with unwinding of approximately one turn of promoter DNA by RNA polymerase (RNAP). By performing parallel experiments with negatively and positively supercoiled DNA, we have been able to deconvolute the change in extension caused by RNAP-dependent DNA unwinding (with ≈1-bp resolution) and the change in extension caused by RNAP-dependent DNA compaction (with ≈5-nm resolution). We have used this approach to quantify the extent of unwinding and compaction, the kinetics of unwinding and compaction, and effects of supercoiling, sequence, ppGpp, and nucleotides. We also have used this approach to detect promoter clearance and promoter recycling by successive RNAP molecules. We find that the rate of formation and the stability of the unwound complex depend profoundly on supercoiling and that supercoiling exerts its effects mechanically (through torque), and not structurally (through the number and position of supercoils). The approach should permit analysis of other nucleic-acid-processing factors that cause changes in DNA twist and/or DNA compaction.

Footnotes

↵ ‡ To whom correspondence on transcription should be addressed. E-mail: ebright{at}waksman.rutgers.edu. §To whom correspondence on nanomanipulation should be addressed. E-mail: strick{at}cshl.edu.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: RNAP, RNA polymerase holoenzyme; NTP, nucleoside triphosphate.