Temperature Dependence and Sequence Specificity of DNA Triplex Formation: An Analysis Using Isothermal Titration Calorimetry

We have investigated the thermodynamics and specificity of DNA triplex formation with isothermal titration calorimetry (ITC). The triplex formation between a 23-mer double-stranded homopurine−homopyrimidine and a 15-mer single-stranded homopyrimidine oligonucleotide forming T·AT and C+·GC triads at pH 4.8 is driven by a large negative calorimetric enthalpy change, ΔHcal, of the order of −80 kcal/mol. ΔHcal is strongly temperature dependent, yielding a heat capacity change, ΔCp, of about −1 (kcal/mol)K-1. The equilibrium association constant, K, obtained from the titration curve is about 9 × 107 M-1 at 25 °C (binding free energy change, ΔG, is about −11 kcal/mol). Thus, the triplex formation is accompanied by a negative entropy change (ΔS = −245 (cal/mol)K-1 at 25 °C). We found that K is insensitive to temperature near room temperature, leading to an apparently small van't Hoff enthalpy change (ΔHvH), in sharp contrast with the large negative ΔHcal. Together, the analyses of the observed temperature dependences of K and ΔH and the large negative ΔCp suggest that the triplex formation is a coupled process between conformational transitions in single-stranded DNA and its binding with double-stranded DNA. The examination of single mismatches in the triplex formation has shown that K and ΔG are not strongly affected by the particular combination of triad sequences (differences in ΔG are within 1.2 kcal/mol). In contrast, single mismatches affected ΔHcal to a greater extent (up to 7-kcal/mol differences). We discuss possible means to enhance specificity in triplex formation, implied by the present findings.