T7 promoter release mediated by DNA scrunching

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Abstract
Transcription initiation includes a phase in which short transcripts dissociate from the transcription complex and the polymerase appears not to move away from the promoter. During this process DNA may scrunch within the complex 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 contacts, or by limits on the amount of DNA that can be scrunched. Using exonuclease and KMnO4 footprinting of T7RNAP transcription complexes we show that the DNA scrunches during progression through initial transcription. To determine whether promoter release is determined by RNA length or by the amount of DNA scrunched, we compared release at promoters where the polymerase is forced to initiate at +2 with those where it initiates at +1. For RNAs of identical length, release is greater when more DNA is scrunched. Release is inhibited when a nick introduced into the template relieves the strain of scrunching. DNA scrunching therefore makes an important contribution to T7 promoter release.