Aptamer-based regulation of DNA polymerase activity for the detection of protein-small molecule interactions

Abstract

Herein, we developed a novel method for identifying protein-small molecule interactions (PSMIs) based on the switching of DNA polymerase activity. This strategy employs the small molecule-linked DNA probe (SMP) that could bind to and disrupt the DNA polymerase aptamer probe (DAP) capable of inhibiting DNA polymerase activity. Without the binding of the target protein, the SMP is readily degraded by the applied exonuclease I (exo I), preventing its binding to the DAP. The DAP then freely inhibits the polymerase activity through its specific binding to the polymerase. In the presence of the target protein, however, the binding between the target protein and the small molecule protects the SMP against the exo I-catalyzed degradation. The intact SMP now binds to the DAP and disrupts its active aptameric structure, preventing the DAP from inhibiting the polymerase activity. The uninhibited DNA polymerase catalyzes the primer extension reaction in conjugation with the TaqMan probe (TP), leading to a significant fluorescence enhancement. Taking advantage of this elaborate design principle, we successfully identified the two model PSMIs, streptavidin/biotin (SA/BTN) and anti-digoxigenin/digoxigenin (ADIG/DIG), as low as 4.01 nM and 6.72 nM, respectively, with excellent specificity. We further validated its practical applicability by reliably identifying the SA/BTN interaction in heterogeneous human serum specimens.