Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching.
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.
Revyakin
Andrey
A
Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
Liu
Chenyu
C
Ebright
Richard H
RH
Strick
Terence R
TR
D001483:Base Sequence; D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012313:RNA / Q000096:biosynthesis; D024363:Transcription Initiation Site / Q000502:physiology; D014158:Transcription, Genetic / Q000502:physiology*
D012313:RNA; D004247:DNA; D012321:DNA-Directed RNA Polymerases