Probing transcription factor binding activity and downstream gene silencing in living cells with a DNA nanoswitch

Transcription factor DNA binding activity is of pivotal importance in living systems because of its primary involvement in the regulation of genetic machinery. The analysis of transient expression levels of transcription factors in response to a certain cell status is a powerful means for investigating cellular dynamics at the biomolecular level. Herein, a DNA-based molecular switch that enables probing of transcription factor DNA binding activity is directly used in living cells. We demonstrate that the DNA nanoswitch allows for dynamic fluorescence imaging of NF-κB and quantification of downstream gene silencing in real time. The present strategy is based on a functional DNA nanodevice that transduces, through a binding-induced conformational change, the recognition of a specific transcription factor into a fluorescent signal. In addition, stochastic optical resolution microscopy, a super-resolution microscopy technique, is used to track the internalization and intracellular trafficking of the DNA nanodevice with high spatial resolution. Overall, it has been shown that a rationally designed DNA nanodevice can be used to achieve rapid, simple, and cost-effective real-time determination of transcription factor binding activity and downstream gene silencing.