Thermodynamics and Kinetics of Base‐Stacking Interactions

The thermodynamics and kinetics of the self‐association of N6, N9‐dimethyladenine has been studied as a model system for base stacking. Molal osmotic coefficients have been determined by vapor pressure osmometry in aqueous solutions at four different temperatures. These data, indicating a very high degree of association much beyond the dimer stage, are consistent with a series of consecutive equivalent association processes. The analysis is performed with an isodesmic model, which allows for cooperativity of the first binding step. Cooperativity can almost be neglected in the present case; the thermodynamic parameters for the formation of stacks are ΔH°=– 8.7 (° 1.5) kcal/mol and ΔS°=– 21.6 cal/K resulting in a stability constant K= 60 at 20°C.The kinetics of base stacking has been investigated by means of sound absorption techniques in the 10–100 MHz frequency range. The excess absorption profiles are only slightly broader than theoretically expected for a single relaxation process. The data can be explained by an isodesmic kinetic model. Formation of stacks proceeds with a rate constant of about 109 M−1 sec−1 and an activation enthalpy of + 6 kcal/mol. Evaluation of the amplitude