transcription bubble formation triggered by bacterial RNAP

The R · Pc → R · Po transition occurs
in three steps. In step I, dsDNA melts and the nontemplate strand
makes stable interactions with RNAP. In step II, DNA scrunches into
RNA polymerase and the downstream base pairs sequentially open
to form the transcription bubble, which results in strain build up.
Subsequently, downstream dsDNA bending relieves the strain as
R · Po forms. Entry of the dsDNA into the active-site channel of
RNAP requires widening of the channel, which occurs by a swing
mechanism involving transient movements of a subdomain of the β
subunit caused by steric repulsion with the DNA template strand. If
premature local melting away from the −10 element occurs first
then the transcription bubble formation is slow involving reformation
of the opened base pairs and subsequent sequential unzipping
as in the fast trajectories.

Category:

Science & Technology

Tags:

• RNAP