Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: thermodynamic evidence for three linked association pathways.

The series of cooperative transitions that lead to [d(TG4)4·(K+)m] quadruplex assembly upon rapid addition of KCl to d(TG4) strands were studied. Quadruplex samples were dialyzed against KCl then Li-EDTA and found to retain between three and five strongly bound potassiums with affinities >106 M-2. Absorbance thermal denaturation (melt) and circular dichroism (CD) equilibrium binding data were obtained. The latter were analyzed using two classes of binding models to simulate the effects of the assumed intermolecular interactions on the binding curves (isotherms). The melt experiments yielded equilibrium dissociation constants (Kd) ranging from 10-11 to 10-12 M3 at the melting temperatures. Extrapolating these values to 23 °C predicts Kd values in the 10-28 M3 range if the heat capacity (Cp) is not strongly dependent upon temperature changes over this range. Assuming Ka is equal to 1/Kd (from melting analyses), very large association free energies stabilize the quadruplex at 23 °C in 100 mM KCl (ΔGa = −43 k...