Biophysical Studies of the c-MYC NHE III 1 Promoter: Model Quadruplex Interactions with a Cationic Porphyrin

Abstract

Regulation of the structural equilibrium of G-quadruplex-forming sequences located in the promoter regions of oncogenes by the binding of small molecules has shown potential as a new avenue for cancer chemotherapy. In this study, microcalorimetry (isothermal titration calorimetry and differential scanning calorimetry), electronic spectroscopy (ultraviolet-visible and circular dichroism), and molecular modeling were used to probe the complex interactions between a cationic porphryin mesotetra (N-methyl-4-pyridyl) porphine (TMPyP4) and the c-MYC PU 27-mer quadruplex. The stoichiometry at saturation is 4:1 mol of TMPyP4/c-MYC PU 27-mer G-quadruplex as determined by isothermal titration calorimetry, circular dichroism, and ultraviolet-visible spectroscopy. The four independent TMPyP4 binding sites fall into one of two modes. The two binding modes are different with respect to affinity, enthalpy change, and entropy change for formation of the 1:1 and 2:1, or 3:1 and 4:1 complexes. Binding of TMPyP4, at or near physiologic ionic strength ([K +] = 0.13 M), is described by a “two-independent-sites model.” The two highest-affinity sites exhibit a K 1 of 1.6 × 10 7 M −1 and the two lowest-affinity sites exhibit a K 2 of 4.2 × 10 5 M −1. Dissection of the free-energy change into the enthalpy- and entropy-change contributions for the two modes is consistent with both “intercalative” and “exterior” binding mechanisms. An additional complexity is that there may be as many as six possible conformational quadruplex isomers based on the sequence. Differential scanning calorimetry experiments demonstrated two distinct melting events ( T m1 = 74.7°C and T m2 = 91.2°C) resulting from a mixture of at least two conformers for the c-MYC PU 27-mer in solution.