Figure 4.

The cRNA promoter within immobilized replication complexes adopts multiple conformations but is not dynamic. (A) The 5′ cRNA adopts a similar stem-loop structure to 5′ vRNA. 5′ vRNA (PDB code: 5MSG) is shown in orange, 5′ cRNA (PDB code: 5EPI) in dark blue, and RNAP (PDB code: 5MSG) in cyan. (B) Fluorophore positions and sequence of the cRNA promoter used in immobilized complexes. (C) Kymograph of time traces from immobilized complexes containing a cRNA promoter labeled with a donor fluorophore at position 17 on the 5′ end and an acceptor fluorophore at position 1 on the 3′ end. E* represents apparent FRET efficiency. Frame time: 100 ms. (D) FRET histogram from (C), fitted with Gaussian curves centered at 0.55 and 0.72. (E, F) Representative time traces showing the lack of transitions between states.