Figure 3.

Structure and properties of extended hammerheads (HHe) against short RNA substrates. (A) Schematic representation of the different ribozyme–substrate complexes. HHe-PLMVd and HHe-ELVd hammerheads contain TSMs, while the minimal HHe-sTRSV-ΔL1 and HHe-ELVd-ΔL1 hammerheads lack these motifs. (B) Diagrams representing the product fraction (F) as a function of time at 10 and 0.1 mM Mg⁺² (left and right, respectively) generated by four different hammerheads: HHe-PLMVd, HHe-ELVd, HHe-ELVd-ΔL1 and HHe-sTRSV-ΔL1. The inset displays the first 10 min of each reaction. (C) Analysis by denaturing PAGE (20%) and autoradiography of reactions catalyzed by four extended hammerheads at 0.1 mM Mg⁺². The positions and size of the 5′-labeled substrates (RF-994 and RF-993) and of the resulting 5′-cleavage products (P) are indicated.