Thermodynamics and structure of a DNA tetraplex: A spectroscopic and calorimetric study of the tetramolecular complexes of d(TG₃T) and d(TG₃T₂G₃T)

We report a combined thermodynamic and structural characterization of a DNA tetraplex. Using spectroscopic and calorimetric techniques, we demonstrate that d(TG₃T) and d(TG₃T₂G₃T), in the presence of K⁺, form stable tetramolecular complexes. From differential scanning calorimetry measurements, we obtain the following thermodynamic profiles for formation of each tetraplex at 25°C: ΔG° = -6.9 kcal/mol of tetraplex (or -2.3 kcal/mol of tetrad; 1 cal = 4.184 J), ΔH° = -62.6 kcal/mol of tetraplex (or -20.9 kcal/mol of tetrad), and ΔS° = -186.9 cal · K^-1 · mol^-1 of tetraplex (or -62.3 cal · K^-1 · mol^-1 of tetrad) for the d(TG₃T) tetraplex; and ΔG° = -20.2 kcal/mol of tetraplex (or -3.4 kcal/mol of tetrad), ΔH° = - 123.2 kcal/mol of tetraplex (or -20.5 kcal/mol of tetrad), and ΔS° = -346.0 cal · K^-1 · mol^-1 of tetraplex (or -57.7 cal · K^-1 · mol^-1 of tetrad) for the d(TG₃T₂G₃T) tetraplex. These data demonstrate that at 25°C a G-tetrad can exhibit considerable stability, comparable to or even exceeding that of most Watson-Crick nearest-neighbor interactions, with this stability resulting from a very favorable enthalpy of formation. Temperature- dependent CD measurements reveal that the melting temperatures of both tetraplexes exhibit unusually low salt dependences. This unexpected behavior may reflect a diminished charge density due to bound K⁺ ions. For each complex, the Na⁺ and K⁺ forms exhibit drastically different isothermal and temperature-dependent CD profiles, with the K⁺ forms of each tetraplex melting more sharply and at a higher temperature than the Na⁺ forms. Using one- and two-dimensional NMR techniques, we show that the strands in the tetramolecular complex of d(TG₃T),K⁺ are all parallel and that the guanine glycosidic conformations are all anti.