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Abstract:
The open promoter complex (OC) is a central
intermediate during transcription initiation that
contains a DNA bubble. Here, we employ singlemolecule
Fo¨ rster resonance energy transfer experiments
and Nano-Positioning System analysis to
determine the three-dimensional architecture of a
minimal OC consisting of promoter DNA, including
a TATA box and an 11-nucleotide mismatched region
around the transcription start site, TATA box-binding
protein (TBP), RNA polymerase (Pol) II, and general
transcription factor (TF)IIB and TFIIF. In this minimal
OC, TATA-DNA and TBP reside above the Pol II cleft
between clamp and protrusion domains. DownstreamDNA
is dynamically loaded into and unloaded
from the Pol II cleft at a timescale of seconds. The
TFIIB core domain is displaced from the Pol II wall,
where it is located in the closed promoter complex.
These results reveal large overall structural changes
during the initiation-elongation transition, which are
apparently accommodated by the intrinsic flexibility
of TFIIB.
