FIG. 1.

D-A labeled promoter constructs representing two reaction coordinates. Examples of dyes’ attachment points in RPo for two reaction coordinates (pdb code: 4XLN). (a) Scrunching coordinates: dyes attached to bases upstream and downstream relative to the transcription bubble; (b) bubble coordinates: dyes attached to bases within the transcription bubble. The arrows show the general directions in which distance changes are expected in the two reaction coordinates. Dye AVs are also shown as green (D) and red (A) partial spheres.