Nuclear magnetic resonance studies of 2'- and 3'-ribonucleotide structures in solution

A systematic 220-MHz proton nuclear magnetic resonance (nmr) study has been made of all common purine and pyrimidine 2'(3')-ribonucleotides in D2O solutions at 20 plus or minus 2 degrees. Spectra for the entire series were measured under similar conditions of concentration, temperature, and ionic strength, thereby facilitating intercomparisons of spectral properties. Spectral assignments were accomplished with the aid of selected 31P-1H decoupling experiments and accurate values of nmr parameters were derived by simulation-iteration procedures. A detailed analysis of the coupling constants and chemical shifts permitted a determination of conformational properties for ribose rings, exocyclic carbinol and phosphate groups, and the orientation of base-ribose rings. Following procedures described elsewhere, an evaluation was made of ribose ring pseudorotational parameters for each 2'(3')-nucleotide. The results show that both the degree of pucker and pseudorotational angle vary only slightly throughout the entire series of molecules, and lie within the ranges found in the crystalline state. Furthermore, the ribose rings are in rapid equilibrium between N type (C(3')-ENDO, C(2')-exo) and S type (C(2')-endo, C(3')-exo) conformers, N forms and is formed by S, with an S type conformer favored in purine 2'(3')-ribonucleotides (-60:40) while pyrimidines exhibit approximately equal compositions. Thus, the phosphate location on the ring has less of an effect on ring properties than the nature of the base ring. An analysis is also reported of rotamer equilibria about C(4')-C(5'), C(2')-O(2'), and C(3')-O(3') bonds. For the former the nmr coupling constant data are consistent with a predominant gg rotamer (-70%) with gt and tg rotamers populated to the extent of -20 and -10%, respectively. No correlation of the type seen for 5'-nucleotides appears to exist between C(4')-C(5') gg population and ribose ring equilibrium composition. For 2'-nucleotides the 31P-H(2') coupling data indicate a preferred C(3')g, C(1')t conformer about C(2')-O(2') in agreement with 13C nmr results. A less definitive rotamer analysis follows from observed J31P,H(3') values, but when these results are combined with relevant chemical shift data for deoxynucleosides and nucleotides the evidence strongly points to essentially free rotation and approximately equal rotamer populations about C(3')-O(3'). Chemical shift differences between purine and pyrimidine 2'(3')-ribonucleotides are qualitatively accounted for by "in-plane" purine diamagnetic anisotropy effects. Also, the greater magnitude for purine deshieldings in 2'(3')-nucleotides relative to 5'-nucleotides is explained by a more favored syn:anti ratio in the former in line with recent nucle