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In the paused state, the polymerase can be stationary at one position on DNA, or it can diffuse backward along the DNA and then recover from these backtracks.
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The measurement cavity is lined with Cd to shield the source against slow neutrons diffusing backward from the moderator.
The backward stepping rate kb is not affected by the nucleosome, because little histone transfer occurs in our experimental geometry where the DNA template is under tension (Hodges et al., 2009; Bintu et al., 2011) and therefore the polymerase does not encounter any roadblock when it diffuses backward.
In this model, Pol II diffuses back and forth on DNA with a forward stepping rate constant kf and a backward stepping rate constant kb during a backtracked pause.
where admits a natural interpretation as backward diffuse phase function and.
The main effect of backward diffuse scattering is seized in the angular width of the lobes, always equal nearly to 20°.
During a pause, Pol II diffuses forward and backward with force-biased rate constants kf and kb, respectively.
Backward connections are more abundant and diffuse than forward connections and their effects are primarily modulatory.
This very diffuse pattern was only found in around 10%% of backward projections, but it was not found in any forward projections.
If, however, the head diffuses to a favorable binding site (13 nm forward), the head strains backward and thus accelerates strong binding in the forward target region based on the search-and-catch model [36].
Backward, march!
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