Syn–anti equilibrium of purine bases in dinucleoside monophosphates as studied by proton longitudinal relaxation

The preferential orientations of the purine bases in dinucleoside monophosphates such as ApA, ApG, and GpA in 10−2M neutral aqueous solutions have been investigated by proton relaxation at 250 MHz. These orientations are deduced from computer simulations of the magnetization recovery curves following a 180° nonselective pulse. The distances between the H(8) proton of a base and the ribose ring protons which are used in these calculations are obtained by minimization as a function of the glycosyl torsion angle ϒ of the standard deviation between the isotropic reorientation correlation times τR derived from the relaxation rates of these protons. The average H(1′) – H(8) distance obtained by this procedure may be readily verified from the reduction of the H(1′) relaxation rate when H(8) is substituted by a deuteron. The limits of validity of the assumption of a single correlation time τR governing the proton relaxation have been estimated, taking into account several possible internal motions, e.g., the rotation of the base, of the methylene exocyclic group and the N ⇄ S interconversion of the ribose ring. For 10−10 < τR < 2 × 10−10 sec, it appears that the influence of these motions on the proton relaxation becomes perceptible when the jump rates among equilibrium positions exceed ca. 109 sec−1. The whole of the experimental results show that for the ribose ring N conformer, the orientation of the bases is found in the ranges 60° < ϒ < 80° (syn) and 180° < ϒ < 210° (anti). For ribose S conformer, it is observed that this orientation is mainly syn with 5° < ϒ < 90°. The average H(1′) – H(8) distance provides semiquantitative information on the overall syn or anti orientations of the base in each nucleoside moiety. At 298 K the population of the anti conformer is found to increase in the order A- pG < Ap-G ∼ Gp-A < Ap-A < A-pA < G-pA. A more detailed analysis of relaxation data shows that the maximum possible fraction of the stacked form of dinucleotides, due to the occurrence of N-anti conformers in both nucleoside moieties, is in the order ApG < GpA < ApA, in agreement with previous works, with however smaller values. Lastly the deuteron linewidth in position 8 of the bases indicates a syn–anti transition rate of the order of 109 sec−1 at room temperature, without noticeable effects therefore on the proton relaxation.