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Thermodynamic analyses of triplex formation with homopurine oligonucleotide
Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
We analyzed the thermodynamics of purine motif triplex formation by isothermal titration calorimetry. The signs of calorimetric enthalpy change, 
Hcal, and entropy change, S, of the triplex formation were negative in the temperature range between 15 and 35 °C. Since an observed negative S was unfavorable for the triplex formation, the triplex formation was driven by a large negative Hcal. Hcal decreased with increasing temperature, yielding a negative heat capacity change, Cp, of approximately –1.2 kcal mol–1 K–1. We found that the binding constant, Ka, increased with increasing temperature, leading to an apparent positive van't Hoff enthalpy change, Hvh, which was in sharp contrast with the large negative Hcal. The analyses of the observed temperature dependence of Ka and Hcal and the negative Cp suggest that the purine motif triplex formation near room temperature is not a simple two-state binding process but exhibits multiple states, which was previously observed for the pyrimidine motif triplex formation near room temperature.