Simple model to account for the deoxy-versus ribodimer stacking quotient data. Estimation of apparent and intrinsic equilibrium quotients for intramolecular stacking association of purine deoxy- and ribodinucleoside monophosphates

Abstract

Stacking equilibrium quotients were evaluated for three purine deoxyribo-dimers, d-ApA, d-m6Apm6A and d-GpG, using procedures developed in earlier studies, and compared with those for the corresponding ribo-dimers. It was shown that the deoxyribo-dimers were apparently more strongly stacked than the corresponding ribo-dimers at 25 degrees C. To explain the observed difference in stability (as measured by the apparent stacking quotient) in the two series of dimers a new extended two-state model is advanced, that the differences in the apparent stacking quotients are due to a limited availability of the number of the sugar-ring puckering modes in the stacked ribo-dimers as compared with the case in the stacked deoxyribo-counterparts. The intrinsic stacking quotients, which are interrelated with the apparent stacking quotients by the microscopic sugar puckering equilibrium constants, were also evaluated for the purine deoxy- and ribo-dimers, and were found to be the same in any pair of these dimers.