FIG. 1.

(color). Loop-mediated gene regulation is tuned by parameters incorporated into a thermodynamic model. (a) Lac repressor reduces gene expression by binding its operators, including binding to both operators and looping the intervening DNA. (b) A thermodynamic model of gene regulation contains the states of the two operator constructs, their associated weights, and the rates of transcription from each state. (c) The model predicts the influence of each parameter on gene expression, as captured in the experimentally measurable quantity repression defined in Eq. (1). (d) 3D plot of repression as a function of number of repressors per cell and the main operator binding energy for ΔF_loop(L)=9k_BT and r₂ = r₃. YFP, yellow fluorescent protein; RNAP, RNA polymerase.