Figure 7. Model for Pol II exploration of RCs.

(A) A Pol II molecule encounters the accessible viral DNA multiple times along one potential route to eventually bind at a promoter. 3D diffusion through the RC is interrupted by binding interactions with the viral DNA (gray circles). (B) Hypothetical comparison of nuclear exploration outside RCs as a function of time and binding energy. A DNA-binding protein in the chromatinized nucleus will encounter nucleosome-free DNA sporadically, making multiple low-affinity interactions before eventually finding a high-affinity site. (C) Inside an RC, the high DNA accessibility might shorten the length of 3D excursions before a DNA-binding protein encounters another region of viral DNA in a low-affinity, nonspecific interaction. This, in turn, may reduce the distance a molecule might diffuse before its next binding event, and increases both the chances of that molecule remaining in close proximity and the chances that it will find a high binding energy interaction.