Investigations on purine and pyrimidine bases stacking associations in aqueous solutions by the fluorescence quenching method. III. Intramolecular association of 9,9'-[1,3-propylene]-bis-2-aminopurine.

General equations relating fluorescence quantum yield and lifetime of a compound with its intramolecular stacking equilibrium and kinetics were derived. Intramolecular stacking association of 9,9'-[1,3-propylene]-bis-2-aminopurine in aqueous solution was examined within the range of temperatures from 0 to 90 degrees C. A two-state thermodynamic model of the association was verified. The stacking enthalpy and entropy can be taken, with a good approximation, as temperature-independent (deltaH equals - 2.0 kcal/mol, deltaS=-3.25 e.u.) although the function deltaG=-0.00886T2 + 8.847 T - 2876 describes more precisely the observed changes of stacking free enthalpy with temperature. The association rate constants were detemined. Activation energy of the reaction (2 kcal/mol) is the same as in the case of association between free 2-aminopurine molecules. It confirms a two-step mechanism of the process. The advantages and shortcomings of the fluorescence quenching method are discussed.