This article describes the synthesis of Thy-(Phe-Phe) and mso-fareast-font-family:"Times New Roman";mso-fareast-language:IT">Thy-(Tyr-Tyr) , line-height:200%;font-family:" times="" new="" roman",serif;mso-fareast-font-family: Batang;mso-fareast-language:KO">two thymine-bearing dipeptides based on L-phenylalanine and L-tyrosine, the circular dichroism (CD), UV and dynamic light scattering (DLS) characterization of their self-assemblies, and a CD study of their interaction with nucleic acids (using homoadenine DNA and RNA) and serum proteins (employing BSA as model protein). DLS studies, alongside with CD and UV investigations conducted on aqueous solutions of the derivatives under different concentration and temperature conditions, showed the formation of extensive molecular architectures with hydrodynamic mean diameters higher than 300 nm, with Thy-(Tyr-Tyr) forming at pH=7.5 particularly large and stable networks, involving multiple units, connected by H-bonding, aromatic and hydrophobic interactions. Finally, the findings of our study suggested that Thy-(Phe-Phe) and 200%;font-family:" times="" new="" roman",serif;mso-fareast-font-family:"times="" roman"; mso-fareast-language:IT">Thy-(Tyr-Tyr) , mso-fareast-font-family:Batang;mso-fareast-language:KO"> very stable in human serum, were able to bind BSA protein altering its secondary structure.