Studies of the conformation of modified dinucleoside phosphates containing 1,N6-ethenoadenosine and 2'-O-methylcytidine by 360-MHz 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformations of dinucleoside phosphates.

Seven dinucleoside monophosphates containing epsilonA (1,N6-ethenoadenosine) and 2'-O-methylcytidine were studied by 360-MHz proton magnetic resonance and compared with unmodified dimers and component monomers at 4, 20, 45, and 75 degrees C. These studies show that the dimers exhibit preference for the gg and g'g' conformations for the C-4'-C-5' and C-5'-O-5' bonds, respectively, and that dimerization induces an increase of the population and inflexibility of the 3'-endo conformations for the ribose ring. Three stacked (or stable) conformations for dimers, I, II, and III, in equilibrium with an unstacked (or open) form in solution, are suggested by dimerization shifts of ribose protons. Conformation I exhibits anti, gg, 3'-endo, phi' = 203 to approximately 211 degrees, omega' = 300 degrees, omega = 290 degrees, g'g', gg, 3'-endo, and anti conformation from the 5' end to the 3' end of the dimer. Conformation II shows anti, gg, 3'-endo, phi' = 203-211 degrees, omega = 30 degrees, omega = 100 degrees, g'g', gg, 3'-endo, and anti conformation. Conformation III is anti, gg, 2'-endo, phi' = 260 degrees, omega' = 50 degrees, omega = 220 degrees g'g', gg, 3'-endo, and anti (x approximately 100 degrees) conformation. The dimers, PupPu and PupPy, prefer conformations I and II, while PypPu and PypPy prefer conformation II. Introduction of epsilonA for the base of -pN induces an increase of conformations II and III, while the epsilonA substitution for the Np- residue induces an increase of conformation I. 2'-O-methylation of the Cp- residue of CpC decreases conformation I and increases conformation II. Based on the stable solution conformations of these dimers, a possible conformation of the anticodon loop is proposed, which is an alternative to the one observed in the crystal of tRNAPhe.