Influence of the 2'-Hydroxyl Group and of 6-N-Methylation on the Conformation of Adenine Dinucleoside Monophosphates in Solution. A Nuclear Magnetic Resonance and Circular Dichroism Study

Abstract

Proton NMR studies at 360 MHz are reported on the adenine dinucleoside monophosphates N6-dimethyladenylyl(3''-5'')-N6-dimethyladenosine .**GRAPHIC**. ApA, rApdA, dAprA and on the methyl phosphate esters of the monomers .**GRAPHIC**. .**GRAPHIC**. Ap and pA. Complete 1H-NMR spectra assignments are given. The dimers were also investigated by means of circular dichroism to obtain accurate thermodynamic parameters of the stacking equilibrium. With the aid of the thermodynamic data NMR coupling constant are extrapolated to values appropriate to the stacked conformers. A modernized version of pseudorotation analysis is used to delineate the conformational behavior of the ribose and 2''-deoxyribose rings. The unmethylated dimers can be arranged in 2 groups (dApdA/dAprA vs. ApA/rApdA) according to their melting temperatures. ApA and the fully N6-methylated dimer .**GRAPHIC**. prefer to adopt the classical right-handed N-N stacked conformation. Both dimers with a 2''-deoxyribose ring at the 5''-OH end (dApdA and dAprA) behave similarly and occur in solution as a 75:25 mixture of S-S and S-N stacked states. The fully stacked hybrids dimer rApdA displays an unexpectedly large amount of S conformers (> 40%) in both sugar rings. This finding is rationalized by the postulation of a right-handed helical S-S stacked state on the basis of NMR and circular dichroic data.