Determination of microscopic ionization constants and microscopic stacking equilibrium quotients of adenylyl(3' --> 5')adenosine.

Using the basic ionization constants for a pair of isomers, m1ApA and Apm1A, and the measured values for the overlapping pK values of ApA, the microscopic ionization constants and intramolecular stacking quotients for the monoprotonated ApA were estimated. The results indicate that, in contrast to the case of GpG, ApA did not exhibit preferential protonation on either site of 3'- and 5'-linked nucleoside bases and neither enhanced nor diminished stacking was observed for ApA and ApA as compared to ApA.