Fig. 1. DNA nanomachine and linear probe schematics. (a) Three-state DNA nanomachine transitions between Relaxed, Closed, and Open states with the addition of fuel strands, F 1 and F 2, and their complements, cF1 and cF2. In the Relaxed state, the distance between the dye and quencher conjugated to double-stranded DNA segments A1 and A2 is estimated to be ∼5 nm. (b) The two-state linear probe transitions between the Bright and Dark states upon hybridization of the dye-labeled probe strand, P, and the quencher-labeled strand, Q. Strand displacement by cQ releases P and restores fluorescence emission. The mechanical states are monitored by measuring the fluorescence emission from the devices.
