Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise

Significance To transcribe DNA sequences into RNA, RNA polymerase (RNAP) first binds to promoter DNA. The promoter sequence dictates both binding strength and rate of remodeling the DNA duplex by RNAP to open 13 base pairs in the start site region. This open “bubble” allows complementary nucleotides to pair with template-strand bases and be incorporated into RNA. All sequence-specific, RNAP-promoter contacts must break for RNAP to escape and elongate the RNA, but how this occurs is not well understood. Here, we report rate constants for each initiation step at the λPR promoter at different temperatures. We analyze these data to obtain insights into which open complex initiates and when RNAP-promoter contacts are disrupted, allowing bubble collapse, duplex formation, and promoter escape.