Figure 1.

Various designs of fluorogenic 8-17 deoxyribozyme. (A) Substrates internally labeled with F and Q. The top strand is the chimeric DNA/RNA substrate in which the lone RNA phosphodiester linkage is denoted as ‘r’. Substrate nucleotides are numbered with respect to ‘r’ as indicated. 8-17 is made up of a 15 nt catalytic core flanked by two substrate-binding arms that form Watson–Crick interactions (small vertical lines) with the substrate. Dot denotes an essential G–T wobble interaction. (B) F and Q are at the opposing termini of substrate and 8-17. (C) F and Q are at either end of the substrate.