Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex

Cell. 1995 May 5;81(3):341-50. doi: 10.1016/0092-8674(95)90387-9.


A central enigma of transcriptional regulation is how the normally efficient transcription elongation complex stops at pause and termination signals. One possibility, raised by the discovery that RNA polymerase sometimes contracts its DNA footprint, is that discontinuous movements contribute to recognizing these signals. We report that E. coli RNA polymerase responds to sequences immediately downstream and upstream from the his leader pause site by changing neither its downstream DNA contact nor its upstream RNA contact for 8 bp preceding the pause. This compressed complex isomerizes to a paused conformation by an approximately 10 bp jump of its downstream DNA contact and simultaneous extrusion of an RNA hairpin that stabilizes the paused conformation. We suggest pausing and termination could be alternative outcomes of a similar isomerization that depend on the strength of contacts to 3'-proximal RNA remaining after the jump.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • DNA, Bacterial / metabolism*
  • DNA-Binding Proteins / metabolism
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli / enzymology*
  • Escherichia coli Proteins*
  • Models, Genetic
  • Molecular Sequence Data
  • Movement
  • Nucleic Acid Conformation
  • Peptide Elongation Factors / metabolism
  • Protein Binding
  • RNA, Bacterial / metabolism*
  • Ribonucleases / metabolism
  • Transcription Factors / metabolism
  • Transcription, Genetic*
  • Transcriptional Elongation Factors


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • GreB protein, E coli
  • Peptide Elongation Factors
  • RNA, Bacterial
  • Transcription Factors
  • Transcriptional Elongation Factors
  • DNA-Directed RNA Polymerases
  • Ribonucleases