Figure 2.

Scrunching during transcription start site selection and initial transcription. RNAP is gray. Promoter DNA nucleotides (nt) are drawn as circles. The numbering is from wild-type rrnB P1. +1 is 9 bp downstream from the -10 hexamer. The -10 hexamer is shown as filled orange circles. Positions of two alternative transcription start sites are indicated as filled circles on the template strand, blue for the TSS 6 bp downstream from the end of the -10 element and red for the wild-type TSS 9 bp from the -10 element. The active site Mg²⁺ is shown as a filled purple circle. A: Scrunching during TSS selection. Two different forms of the open complex are shown. Top, non-scrunched complex results in a TSS 6 bp downstream from the -10 hexamer [1, 21]. Bottom, 3 nt of DNA are pulled into RNAP past the active site, resulting in a scrunched open complex and a TSS 9 bp downstream from the -10 hexamer. B: Scrunching during initial transcription. The proposed change in the DNA path during the transition from RP_O (top) at an rrnB P1 promoter variant with a TSS of +6 with respect to the end of the -10 hexamer [21], to an initial transcribing complex with a 5 nt RNA (RP_ITC5, bottom). RNA nt are shown as filled green circles. Similar structural changes occur during initial transcription and during TSS selection. In each case, interconversion between the scrunched and unscrunched forms is likely to occur.