Calorimetric analysis of triple helices targeted to the d(G3A4G3).d(C3T4C3) duplex.

We present a thermodynamic analysis based on differential scanning calorimetry (DSC) of three short intermolecular DNA triplexes targeted to the same DNA duplex: d(C+3T4C+3)*d- (G3A4G3).d(C3T4C3) (PYR), d(G3A4G3)*d(G3A4G3).d(C3T4C3) (PUR), and d(G3T4G3)*d(G3A4G3).d(C3T4C3) (PUR/PYR). Enthalpies, delta H, and entropies, delta S, are measured by model-free integration of the DSC curves and are compared to the same quantities determined by van't Hoff analysis of the DSC curves and, in the case of the PYR and PUR/PYR triplexes, UV melting curves as well. In the case of the PUR triplex, which exhibits monophasic melting behavior, the calorimetric delta H and the calorimetrically determined van't Hoff delta H are in excellent agreement, indicating an all-or-none transition for this triplex. For the PYR and PUR/PYR triplexes, which melt in a biphasic manner, the calorimetrically determined van't Hoff delta H values are somewhat larger than the model-independent calorimetric delta H values. In those cases, however, good agreement is found between the calorimetric delta H values and the spectrophotometrically determined van't Hoff delta H values. The calorimetrically determined delta H values, expressed per mole of triplet, for the three triplexes are 4.5, 3.8, and 2.4 kcal/mol for the PUR, PYR, and PUR/PYR triplexes, respectively. The same order of stability is observed in terms of delta G and Tm values. The high stability of the PUR triplex at neutral pH indicates that purine oligonucleotides may be the most effective at targeting duplex regions for triple helix formation in vivo.