We present a versatile biosensing strategy that uses nucleic acids programmed to undergo an isothermal toehold mediated strand displacement in the presence of analyte. This rearrangement results in a double biotinylated duplex formation that induces the rapid aggregation of streptavidin decorated quantum dots (QDs). As biosensor reporters, QDs are advantageous to organic fluorophores and fluorescent proteins due to their enhanced spectral and fluorescence properties. Moreover, the nanoscale regime aids in an enhanced surface area that increase the number of binding of macromolecules, thus making cross-linking possible. The biosensing transduction response, in the current approach, is dictated by the analysis of the natural single particle phenomenon known as fluorescence intermittency, or blinking is the stochastic switching of fluorescence intensity ON (bright) and OFF (dark) states observed in single QD or other fluorophores. In contrast to binary blinking that is typical for single QDs, aggregated QDs exhibit quasi-continuous emission. This change is used as an output for the novel biosensing techniques developed by us. Analysis of blinking traces that can be measured by laser scanning confocal microscopy revealed improved detection of analytes in the picomolar ranges. Additionally, this unique biosensing approach does not require the analyte to cause any fluorescence intensity or color changes. Lastly, this biosensing method can be coupled with therapeutics, such as RNA interference inducers, that can be conditionally released and thus used as a theranostic probes.