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-degrees-C: DELTA-G-degrees = -6.9 kcal/mol of tetraplex (or -2.3 kcal/mol of tetrad; 1 cal = 4.184 J), DELTA-H-degrees = -62.6 kcal/mol of tetraplex (or -20.9 kcal/mol of tetrad), and DELTA-S-degrees = - 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 DELTA-G-degrees = -20.2 kcal/mol of tetraplex (or -3.4 kcal/mol of tetrad), DELTA-H-degrees = -123.2 kcal/mol of tetraplex (or -20.5 kcal/mol of tetrad), and DELTA-S-degrees = -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-degrees-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.