We report that single-stranded (ss) DNA aptamers can be activated by counterions such as dodecylguanidinium (DG) to act as transporters in fluorogenic vesicles. However, their activity is independent of the presence or absence of the analyte. Dimerization into ds-DNA helices increases activity in an overadditive manner. Duplex disassembly in response to analyte binding is thus detectable as inactivation. Shortened and mismatched antiaptamers destabilize the active duplex, reduce activity, and increase the sensitivity for the analyte. Supramolecular polymerization of aptamer/antiaptamer duplexes with "sticky ends" is shown to further increase activity without losses in sensitivity for the analyte. The results demonstrate that the principles of DNA nanotechnology are directly applicable to membrane based sensing systems with high precision and fidelity.