IR study of base stacking interactions

For D2O solutions of 1,3-dimethyluracil, cytidine, caffeine, inosine and 2'-deoxyadenosine the concentration dependence of IR spectra (1800-1400 cm-1) have been found which reflects stacking association of these compounds. A method is proposed to use this data to obtain thermodynamic parameters of association and the molecular spectra in the monomer and associated forms. The homoassociation constant for 1,3-dimethyluracil was estimated as k=0.65. Stacking is shown to change radically the spectra, inducing a high-frequency shift of carbonyl vibrations and a decrease in the intensity of skeletal stretching vibration bands. This allows one to distinguish between the stacking interactions and hydrogen bonding. A conclusion is made about the considerable contribution of stacking interactions into the change of IR spectra of DNA and other polynucleotides following conformational transitions.