Schematic representation of hammerhead ribozyme (HHR) for specific cleavage of substrate RNA subjected to substitutional RNA editing. Ribozyme and substrate RNA are shown as black and gray lines, respectively. Dashed lines indicate the base-pair interactions. Ribozyme contains three helices: Helix I and Helix III are in the hybridizing arms for recognizing the target sequence, and Helix II is in the catalytic core. On the substrate RNA, the cleavage site and editing site are denoted by gray and black circles, respectively. To introduce the ability for editing-specific cleavage into the HHR, the recognition base (shown as a circle with dotted outline) is designed to pair only with the edited base at the editing site. In this study, the recognition base C was used for A-to-I editing, and A was used for C-to-U editing. Position of the 5′-NHH-3′ triplet for HHR specificity is shown in this figure, where N is any nucleotide, and H is either A, C, or U. D is any nucleotide except C.
