FIGURE 7.

In vivo DNA looping by Lac repressor and the in vitro challenge. (A) Data from Müller et al.¹⁰¹ showing repression as a function of distance between operators. (B) Change in looping free energy obtained from the Müller-Hill data (black) and theoretical prediction of the energy of cyclization of a DNA molecule based on the worm like chain model¹⁰⁴ and assuming a volume for E. coli of V_cell ≈ 1 μm³ such that ΔF_cyclization = −ln(J_cyclization V_cell). Note that the minima in the two curves do not coincide, suggesting that the effective looping free energy in vivo is not the same as the bare looping free energy deduced from in vitro cyclization measurements. In addition, there is an overall shift in the scales in the two cases. (Inset, B) Difference in the magnitude of the twist modulation between the looping energy obtained from the Becker et al.¹⁰³ data and the theoretical cyclization energy based on harmonic deformations of the base steps.⁷⁵