Adenosine-induced elimination of redox intercalators from dsDNA-aptamer conformational switches

Immobilization and electrochemical characterization of specially designed DNA-aptamer constructs (namely, “DNA conformational switches”) are of great importance for the development of versatile biosensorsand the fundamental understanding of DNA-ligand interactions. Wehave created andimmobilizedadsDNA-anti-adenosine aptamer construct on gold which is expected to undergo structural changes upon binding adenosine.In particular,methylene blue (MB), a solution-diffused redox marker, was used as a model system to probe the rather complex interaction modes between small redox molecules and surface-bound DNA switches. Besides intercalating with the double-stranded DNA stem, MB can stack with a single guaninebase in the relatively unstructured aptamer domain or electrostaticallybindtothe DNA backbone. The decreased surface density of MB after adenosine binding indicated that the ligand-gated structural change of the dsDNA-aptamer construct can eliminate MB molecules that were originally bound to the aptamer domain, but not those in the complementary stem.