Solution structure of the 3'-5' cyclic dinucleotide d(pApA). A combined NMR, UV melting, and molecular mechanics...

The 3'-5' cyclic dinucleotide d(pApA) was studied by means of 1H and 13C NMR experiments, UV-melting experiments, and molecular mechanics calculations. The 1H and 13C NMR spectra were analyzed by means of 2-dimensional NMR experiments. J-Coupling analysis of the 1D and 2D 1H and 13C spectra was used to determine the conformation of the ring systems in the molecule. It appeared that at low temperature (283 K) the deoxyribose sugars adopt a N-type conformation. The geometry is best described by an intermediate between the 3(2)T and 3E forms. In addition, we were able to derive all other torsion angles in the phosphate backbone ring system, i.e., alpha +, beta t, gamma +, delta (= 89 degrees), epsilon t, and zeta +. When the molecule is subjected to an energy minimization procedure (using the program AMBER), the sugar ring system retains, practically speaking, the torsion angles found from the NMR experiments, while the torsion angles around the glycosidic bond adopt a value of 175 degrees in the minimum energy conformation. UV-melting experiments indicate that two molecules can form a dimer in which the adenine bases are intercalated. The feasibility of this structure is indicated by molecular mechanics calculations. At higher temperatures the dimer is converted into separate monomers. In the monomer form the sugars exhibit S-pucker 20% of the time. Concomitantly with the conversion of the N- to the S-conformation, the torsion angles alpha and gamma change.