The stacking interactions of tyrosine methylester (TyrOMe)-guanosine-5'-monophosphate (GMP), TyrOMe-7-methylguanosine-5'-monophosphate (m7GMP), phenylalanine methylester (PheOMe)-GMP and PheOMe-m7GMP pairs in neutral buffer solution have been studied by proton nuclear magnetic resonance (¹H-NMR). The H8 proton signal of GMP showed no noticeable temperature dependence, while the signals of other protons showed usual dependences arising from the ring stacking interaction with aromatic amino acids. The results can be interpreted in terms of the intramolecular C-H…O hydrogen bonding and ring stacking. Complex formations in 1 : 1 molar ratio were deduced for all pairs from their Job plots. The association constant for each pair was obtained by analysis of the Scatchard plot. Further, the van't Hoff plot provided thermodynamic parameters of the complex structure. The analyses of these data suggested that albeit the N-quaternization of GMP strengthens the stacking interaction with aromatic amino acid, the bulky methyl group in m7GMP facilitates the dissociation from the amino acid with small environmental change. The possible conformations of GMP and m7GMP in the interaction states are discussed on the basis of the coupling constants.