To develop non-cationic vectors for gene delivery, a novel class of thymidine-based amphiphiles have been constructed. These molecules showed good biocompatibility. Their complexation with polyadenylic acid through hydrogen bonding and π–π stacking interaction was demonstrated by gel electrophoresis, capillary electrophoresis, transmission electronic microscopy (TEM) and molecular dynamics simulation. It was also found that their biocompatibility and binding ability with DNA varied inversely with the length of the alkyl chains.