Figure 5.

Fluorogenic DNAzymes obtained from random-sequence DNA libraries. (a) The chemical transformation catalyzed by these DNAzymes. These DNAzymes cleave a phosphodiester bond using a nearby 2′-hydroxyl (light blue) as the nucleophile. The special nucleic acid substrate to be cleaved has two features: (1) it contains a single ribonucleotide (riboA) as the cleavage site embedded in a DNA sequence, and (2) the cleavage site is immediately sandwiched between two DNA nucleotides modified with a fluorophore (F; specifically fluorescein) and a quencher (Q; specifically DABCYL). (b) Secondary structures of two representative signaling DNAzymes. rA: adenine ribonucleotide (the cleavage site; shown in blue); F, fluorescein-modified dT; Q, DABCYL-modified dT. Conserved nucleotides are shown in black circles. The substrate strands are shown in red.