Figure 5.

Structure-function studies of F-8. (A) Sequence in the structure of F-8 that were extensively varied. (B) Structure of F-8(X), a variant of F-8 lacking the hairpin but retaining cleavage activity. The catalytic core comprises 16 nt. (C) Sequence and structure of F-8-ATP, a variant of F-8 carrying an ATP-binding aptamer in the hairpin region intended to place the cleavage activity under allosteric regulation by ATP. (D) PAGE analysis of DNA substrate cleavage by F-8-ATP. Reactions were carried out for 4 h under standard conditions in the presence of 50 μM H₂O₂ and the indicated concentrations of ATP. Lane 1, 5′-³²P-labeled DNA substrate. Lane 2, cleavage of F-8-ATP in the absence of additional ATP; lanes 3–8, cleavage reactions in the presence different concentrations of additional ATP. Cleavage assays were under standard single-turnover conditions (about 1 μM deoxyribozyme combined with 10 nM substrate).