Inherent bistabilities within DNA-assembled fluorescent resonant energy transfer systems demonstrated time-varying optical signals in responseto an electrophoretic driving force. Frequency responses of electrophoretically driven FRET systems were shown to be sequence specific.Integration of these signals over time gave near single-molecule sensitivity within a high background of autofluorescence. This researchsuggests that externally driven nanoscale mechanical systems may help improve information flow within morphologically intact specimens.