Energetic differences between the specific binding of a 40 bp DNA duplex and the lac promoter to lac repressor protein

The energetics of LRP binding to a 104 bp lac promoter determined from ITC measurements were compared to the energetics of binding to a shorter 40 bp DNA duplex with the 21 bp promoter binding site sequence. The promoter binding affinity of 2.47 ± 0.01 × 107 M−1 was higher than the DNA binding affinity of 1.81 ± 0.67 × 107 M−1 while the binding enthalpy of −804 ± 41 kJ mol−1 was lower than that of the DNA binding enthalpy of −145 ± 16 kJ mol−1 at 298.15 K. Both the promoter and DNA binding reactions were exothermic in phosphate buffer but endothermic in Tris buffer that showed the transfer of four protons to LRP in the former reaction but only two in the latter. A more complicated dependence of these parameters on temperature was observed for promoter binding. These energetic differences are attributable to additional LRP–promoter interactions from wrapping of the promoter around the LRP.