[Nuclear magnetic resonance study of the conformational situation in an aqueous solution of dinucleoside phosphates]

The strategy of quantitative study of conformational situation in aqueous solutions of dinucleoside phosphates (DNP) has been proposed. It includes the following steps: (1) conformational calculation of stacking conformers (SC) of DNP; (2) measurement of thermodynamic parameters of conformational equililbrium; (3) determination of extensive parameters of stacking state (SS) on the basis of experimental data and thermodynamic parameters; (4) computation of extensive parameters of SC on the basis of the calculated geometry of SC and theoretical concepts of experimental method; (5) comparison of experimental parameters of SS with the calculated ones of SC to establish the SC participating in the equilibrium as well as its relative weights. This strategy was exemplified by ApA, ApC, CpA and CpC. The chemical shifts, spin-spin coupling constants and spin-lattice relaxation rates of DNP protons were used. The predominant SC was found to be related to Pba type with a large twirl angle (45-54 degrees) and almost parallel base planes. For all DNP the presence in equilibrium of left-handed forms was typical. These were Mab forms for ApA, Mbb forms for CpC and CpA, Mbb and Mab forms for ApC. About 10% of SS of ApA and CpA were presented by SC with trans-conformation of C(4')-C(5') bond of oN-part. The SC with C(3')-endo, C(3')-endo combination of ribose conformations were basic for ApA, ApC and CpA, and the only possible for CpC. In case of ApA, ApC and CpA the conformers with C(3')-endo, C(2')-endo sugar combination were presented.