Harnessing a Fluorescent Nucleobase Surrogate for Supramolecular FRET-Aptamer Detection and Target-Site Mapping

DNA aptamers can bind small molecule ligands with high affinity and specificity to produce a unique supramolecular structure. Methods to obtain structural information about the binding interaction coupled with sensitive diagnostics is a gold standard for aptasensor design. However, most sensing strategies afford ligand detection without structural insight, while NMR- or crystallography-based structural methods lack sensitivity required for diagnostics. FRET-based strategies can afford both, especially with internal fluorescent nucleobase probes that are spatially fixed within the helix, but dual aptamer labeling can compromise aptamer affinity toward its target. Herein, we showcase a nucleobase surrogate-ligand FRET-based strategy that affords target-site mapping combined with sensitive target detection that addresses these challenges. A fluorescent molecular rotor (FMR) thiophene chalcone (Th6HI) nucleobase surrogate was incorporated into the tetracycline (TC) 42-mer DNA binding aptamer OTC2 to serve as an acceptor for the TC donor. Time-resolved fluorescence anisotropy experiments predict a compact prefolded OTC2 aptamer that is hardly impacted by TC binding. Consequently, direct excitation of the internal FMR Th6HI at 530 nm affords little response to TC binding, as probe rigidity is not strongly altered. In contrast, indirect excitation of the Th6HI probe through TC donor excitation at 378 nm affords site-dependent sensitized fluorescence (<i>F</i>_sen) of the Th6HI acceptor to afford enhanced sensitivity for TC detection compared to a native platform, which utilizes the intrinsic TC fluorescence. Furthermore, the FRET response provides target-site mapping to build a new binding model for the TC-OTC2 complex that is akin to the three-helical structure of the hammerhead ribozyme.