Open AccessThermodynamics and Kinetics of Base‐Stacking Interactions
Author(s) -
Pörschke Dietmar,
Eggers Frieder
Publication year - 1972
Publication title -
european journal of biochemistry
Language(s) - English
Resource type - Journals
eISSN - 1432-1033
pISSN - 0014-2956
DOI - 10.1111/j.1432-1033.1972.tb01791.x
Subject(s) - isodesmic reaction , molality , thermodynamics , cooperativity , stacking , chemistry , enthalpy , kinetics , relaxation (psychology) , absorption (acoustics) , atmospheric temperature range , vapor pressure , aqueous solution , materials science , standard enthalpy of formation , organic chemistry , psychology , social psychology , biochemistry , physics , quantum mechanics , composite material
The thermodynamics and kinetics of the self‐association of N 6 , N 9 ‐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 Δ H °=– 8.7 (° 1.5) kcal/mol and Δ S °=– 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 10 9 M −1 sec −1 and an activation enthalpy of + 6 kcal/mol. Evaluation of the amplitudes leads to a volume change of 6.8 ml (at 25°C) per mol of stacking sites. The volume change decreases with increasing temperature. Optical measurements in a pressure cell show that the volume decreases with increasing number of stacks. These results are discussed with respect to current theories of base stacking. Both Δ H and Δ V found for the stacking equilibrium are in contrast to the thermodynamic parameters of hydro‐phobic interactions according to the standard view. The present data demonstrate a characteristic difference of hydrophobic interactions between unpolar, unpolarisable particles like simple hydrocarbons and between compounds like nucleic acid bases with high polarisability and a dipole structure.