DISCONTINUOUS MOVEMENTS OF DNA AND RNA IN RNA-POLYMERASE ACCOMPANY FORMATION OF A PAUSED TRANSCRIPTION COMPLEX

A central enigma of transcriptional regulation is how the normally eff icient 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 movement s contribute to recognizing these signals. We report that E. coli RNA polymerase responds to sequences immediately downstream and upstream f rom the his leader pause site by changing neither its downstream DNA c ontact nor its upstream RNA contact for 8 bp preceding the pause. This compressed complex isomerizes to a paused conformation by an similar to 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 is omerization that depend on the strength of contacts to 3'-proximal RNA remaining after the jump.