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Nucleic Acids Research, 1980, Vol. 8, No. 13 3029-3042
© 1980

CHEMISTRY

IR study of base stacking interactions

A.A. Maevsky and B.I. Sukhorukov

Institute of Biological Physics, USSR Academy of Sciences Pushchino, Moscow Region 142292, USSR

Received May 12, 1980. 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 DRA and other polynucleotides following conformational transitions.


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