Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

Aptamers are a class of bioreceptors used in analytical tools dedicated to molecular diagnostics due to their ability to perform structural reorganization upon target binding. However, there is a lack of methodologies allowing to rationalize their structure in order to improve their transduction efficiency. We chose here, a three-strand DNA structure as probe anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to Ampicillin (AMP). Using a set of computational techniques, we investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates for the first time the ability of computational investigations to drive, in-silico, the design of aptasensors.