Design Variations for an Aptamer-Based DNA Nanodevice

The performance of DNA nanodevices based on a thrombin-binding DNA aptamer is strongly dependent on chemical modifications and extensions of the protein-binding core sequence. We here give an overview of the influence of fluorescent labeling and extension of the aptamer device sequence on its binding properties. Sequence extension on the 5′ end as well as labeling on the 5′ or 3′ end does not significantly reduce the binding capabilities. Sequence extension on the 3′ end completely suppresses binding. This knowledge can be utilized for the construction of a doubly labeled aptamer device which can be operated as a switchable molecular beacon.