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. Author manuscript; available in PMC: 2012 Jan 15.
Published in final edited form as: Anal Biochem. 2010 Sep 21;408(2):269–276. doi: 10.1016/j.ab.2010.09.020

Figure 2.

Figure 2

Four possible outcomes of the FID process are depicted. Initially, TO-PRO has negligible fluorescence in the absence of RNA. The dye displays a 500-fold increase in fluorescence intensity in the presence of structured RNA. In the first scenario, the dye is displaced by a ligand, leading to a loss in dye fluorescence. In the second scenario, the ligand and dye have different binding sites, such that no change in fluorescence is observed. In the third case, the ligand and dye have overlapping binding sites, such that fluorescence is quenched. In case 4, the ligand has no affinity for the RNA target, such that TO-PRO remains bound to the RNA and the fluorescence intensity remains the same.