Molecular orientation in the stacked dimer form of 5"AMP in aqueous solution. A study by the NMR-desert method.

Molecular orientation of 5"-AMP in its stacked dimeric form in neutral aqueous solutions has been investigated at room temperature through the NMR-DESERT method proposed earlier by Akasaka et al. (J. Magn. Resonance, (1975) 18, 328-343). The effect of deuterium substitution of H8 of the adenine ring on the relaxation rate of H2 has become appreciable with increasing concentration of 5"-AMP, which should be attributed to the intermolecular H2-H8 interaction between adjacent adenine rings in the stacked dimer of 5"-AMP. The reciprocal sixth-power-averaged distance between H8 and H2 of the adjacent adenine rings in the stacked dimeric form obtained from the differential relaxation rate for H2 has been found to be almost constant (3.6 +/- 0.2 A S.D.) in the whole concentration range studied (0.1--1.0 M). The result has presented a direct proof of the existence of trans-stacking with a relatively large proportion (more than 60%) in the stacked dimeric form of 5"-AMP.