Linking pH, Temperature, and K⁺ Concentration for DNA i-Motif Formation

The conformation a particular DNA segment assumes depends upon its sequence context and the environment under which it is prepared. To complement our findings with G-rich sequences related to the human telomere, we have been investigating the pH induced transition from single strand to i-motif for sequences related to the human telomere C-rich strand. We have carried out titrations of (CCCTAA)₄ from pH 7.0 to pH 5.0 at temperatures ranging from 15 to 45 °C at 115 mM K⁺ and at K⁺ concentrations ranging from 15 to 215 mM at 25 °C. Circular dichroism (CD) spectra were determined to monitor the transition. The pH at the midpoint of the proton induced transition, pH_mp, is dependent upon both temperature and [K⁺]. Wyman-type plots of log K vs pH yielded linear correlations and the slopes of those lines, ΔQ, were also linearly dependent on [K⁺] and T. For these studies, ΔQ represents the minimum number of protons that must be added to the oligomer to induce the initial folding. These results are consistent with Le Chatelier's principle. Optical melting studies were also carried out for (CCCTAA)₄ at pH 5.0 and [K⁺] ranging from 15 to 315 mM. Linear correlations between the temperature at the midpoint of the transition, T_m, and log [K⁺] allowed determination of the differential ion binding term, Δn_K+. These linkages between pH, temperature, and [K⁺] can be utilized to design i-motif forming DNA oligomers with highly tunable properties.