Molecular recognition of the guanidinium/phosphate pair was investigated at microscopic interfaces of aqueous micelles and bilayers. Monoalkyl and dialkyl amphiphiles with guanidinium head groups were synthesized and dispersed in water to form micelles and bilayers having guanidinium groups at the aggregate surface. Binding of nucleotides such as AMP to these functionalized aggregates was evaluated by using an equilibrium dialysis (ultrafiltration) method. The observed binding constants of 10(2)-10(4) M(-1) are much larger than the corresponding binding constant reported for a monomerically dispersed pair in the aqueous phase (1.4 M(-1)) but are smaller than those found at the macroscopic air-water interface (10(6)-10(7) M(-1)). Therefore, the macroscopic interface promotes guanidinium-phosphate interaction more effectively than the microscopic interface. The present finding indicates that the microscopic interface can strengthen hydrogen bonding and/or electrostatic interaction even in the presence of water. Saturation binding phenomena were different between micelles and bilayers. All of the guanidinium groups in fluid micelles are effective for phosphate binding, but part of the guanidinium group in bilayers are not effective probably because of steric restriction.