Investigating a Quadruplex−Ligand Interaction by Unfolding Kinetics

Abstract

We have investigated the interaction of the intramolecular human telomeric DNA G-quadruplex with a hemicyanine−peptide ligand, by studying the rate of quadruplex opening with a complementary DNA oligonucleotide. By employing a minimal kinetic model, the relationship between the observed rate of quadruplex opening and the ligand concentration has enabled estimation of the dissociation constant. A van't Hoff analysis revealed the enthalpy and entropy changes of binding to be −77 ± 22 kJ mol^-1 and −163 ± 75 J mol^-1 K^-1, respectively. Arrhenius analyses of the rate constants of opening free and bound quadruplex gave activation energies of 118 ± 2 and 98 ± 10 kJ mol^-1, respectively. These results indicate that the presence of the ligand has only a small effect on the activation energy, suggesting that the unbinding of the ligand occurs after the transition state for quadruplex unfolding.