T7 promoter release mediated by DNA scrunching

Transcription initiation includes a phase in which short transcripts dissoc iate from the transcription complex and the polymerase appears not to move away from the promoter. During this process DNA may scrunch within the comp lex or the polymerase may transiently break promoter contacts to transcribe downstream DNA. Promoter release allowing extended downstream movement of the polymerase may be caused by RNA-mediated disruption of promoter contact s, or by limits on the amount of DNA that can be scrunched. Using exonuclea se and KMnO4 footprinting of T7RNAP transcription complexes ve show that th e DNA scrunches during progression through initial transcription. To determ ine whether promoter release is determined by RNA length or by the amount o f DNA scrunched, we compared release at promoters where the polymerase is f orced to initiate at +2 with those where it initiates at +1. For RNAs of id entical length, release is greater when more DNA is scrunched. Release is i nhibited when a nick introduced into the template relieves the strain of sc runching. DNA scrunching therefore makes an important contribution to T7 pr omoter release.