The monolayer behavior of nucleolipids 5 ' -stearoyl-uridine (1) and 1 ' ,2 ' -bis [( 1-thyminyl)propionyloxy]-propyl octadecanoate (2) on pure water and aqueous 1 and 5 mM adenosine solutions was investigated by means of surface pressure-molecular area (jc-A) isotherms, which indicate that the structure of the headgroups has a strong influence on the molecular recognition capabilities. The nucleolipid 1 monolayer shows no distinct expansion effect after the recognition effect occurred between the monolayer and the complementary base in the subphase except for an increase of collapse pressure, whereas nucleolipid 2 exhibits a distinctly different surface behavior on aqueous adenosine subphases than on pure water because of its dicephalic structure and the increasing hydrophilicity after the recognition effect occurred. High-quality Fourier transform surface-enhanced Raman scattering spectra indicate that the adenosine molecules in the subphase were transferred onto solid substrates by the Langmuir-Blodgett (LB) technique as a result of the formation of Watson-Crick base pairing at the air/water interface. The LB films deposited from different subphases provide a suitable matrix to investigate the photodimerization of uracil or thymine moieties under ultraviolet irradiation. The photoactivity of uracil and thymine moieties decreased after the recognition effect occurred between the monolayer and the complementary base in the subphase because of an increase of steric hindrance, and prolonged irradiation time is required to accomplish the dimerization. The structure of the headgroups is a determinative factor for controlling the occurrence of intermolecular (nucleolipid 1) or intramolecular (nucleolipid 2) photodimerization.