Three common arrangements of fluorophore (F) and quencher (Q) in the design of fluorescent RNase DNAzyme-based biosensors. F and Q are appended to the nucleobases that flank the cleavage site (a), placed at the end of duplex formed between the substrate and DNAzyme strands (b), or located at the end of the hairpin-shaped substrate strand (c). DNAzyme and substrate strands are shown in black and red, respectively. The cleavage site is marked by a blue “R”.
