A direct fluorescence polarization (FP) assay strategy, dedicated to the small molecule sensing and based
on the unique induced-fit binding mechanism of end-labelled nucleic acid aptamers, has been recently
developed by our group. Small target binding has been successfully converted into a significant increase of
the fluorescence anisotropy signal presumably produced by the reduction of the local motional freedom
of the dye. In order to generalize the approach, a rational FP sensor methodology was established herein,
by engineering instability in the secondary structure of an aptameric recognition element. The antiadenosine
DNA aptamer, labelled by a single fluorescein dye at its 3 extremity, was employed as a model
functional nucleic acid probe. The terminal stem of the stem-loop structure was shortened to induce a
destabilized/denatured conformation which promoted the local segmental mobility of the dye and then a
significant depolarization process. Upon target binding, the structural change of the aptamer induced the
formation of a stable stem-loop structure, leading to the reduction of the dye mobility and the increase
in the fluorescence anisotropy signal. This reasoned approach was applied to the sensing of adenosine
and adenosine monophosphate and their chiral analysis.