FIG. 4.

(color). Correcting for direct upstream repression when calculating looping energies. (a) Regulatory interactions occur between RNA polymerase and the Lac repressor bound to a nearby upstream operator, skewing in vivo measurements of looping based on gene expression. (b) To account for direct auxiliary repression in looping constructs, we measure r₃=r₂, at each operator distance. (c) Correcting the two operator model from Fig. 1(b) to account for direct auxiliary repression reveals increased looping energies for the shortest loops and restores a uniform periodicity of repression with length at short operator distances. Error bars represent standard error.