Secondary structure of the spliceozyme, based on the group I intron ribozyme from <i>Tetrahymena</i>.

<p>(<b>A</b>) Before the reaction, the substrate consists of two exons (red) and an intervening intron (blue). The spliceozyme (black) uses its 5′-terminus to form the P1 duplex, the P1 extension (P1ex), and the 5′-duplex to position the substrate 5′-splice site (filled triangle). The ribozyme 3′-terminus forms the P9.2 duplex and the P9.0 duplex to position the substrate 3′-splice site (empty triangle). (<b>B</b>) After two transphosphorylation reactions the 5′-exon and the 3′-exon of the substrate are joined. The 5′-terminus of the intron is capped by an exogenous G (black) and the 3′-terminus of the intron is liberated. The sequences correspond to the removal of an intron from splice site 258 of the <i>CAT</i> pre-mRNA used in this study. The internal sequence of the intron is drawn as a bold blue line. Note that a hairpin terminator is added to the 3′-terminus for all reactions in cells. The secondary structure of the ribozyme is based on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101932#pone.0101932-Cech2" target="_blank">[58]</a> with the alteration that the P4-P6 domain was positioned on the right side for clarity.