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: Δ G⚬= -6.9 kcal/mol of tetraplex (or -2.3 kcal/mol of tetrad; 1 cal = 4.184 J), Δ H⚬= -62.6 kcal/mol of tetraplex (or -20.9 kcal/mol of tetrad), and Δ S⚬= -186.9 cal· K-1· mol-1of tetraplex (or -62.3 cal· K-1· mol-1of tetrad) for the d(TG3T) tetraplex; and Δ G⚬= -20.2 kcal/mol of tetraplex (or -3.4 kcal/mol of tetrad), Δ H⚬= -123.2 kcal/mol of tetraplex (or -20.5 kcal/mol of tetrad), and Δ S⚬= -346.0 cal· K-1· mol-1of tetraplex (or -57.7 cal· K-1· mol-1of 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.