A novel linear molecular beacon based on DNA-scaffolded silver nanocluster for DNA detection via exonuclease III-assisted cyclic amplification

Abstract

Developing label-free molecular beacon (MB)-based methods for DNA detection has been of great significance in bioanalysis because of their simplicity, low cost, and specificity. In this work, we have developed a novel DNA-scaffolded silver nanocluster linear molecular beacon (AgNC-LMB)-based strategy for sequence-specific DNA detection via exonuclease III (Exo III)-assisted signal amplification. The proposed method involves two processes: target-mediated digestion by Exo III and the synthesis of AgNC-LMB as a switch for signal output. Upon hybridization of the rationally designed probe with target, Exo III, removes nucleotides from 3′ terminus of the probe. The resultant fragment acts as a favorable template to form highly fluorescent DNA/AgNCs. The resulting fluorescence enhancement of the AgNCs provides a quantitative readout proportional to the target concentration in the range of 5 to 300 nM with an LOD of ∼3.2 nM. This method is simple, cost-effective, highly selective, and free of modification or separation.