(A) Schematic depiction of the secondary structure of the ai5γ group II intron from the Saccharomyces cerevisiae mitochondrial COX I gene. Domains 1–6 extend from the central “wheel.” The segments involved in tertiary interactions contributing to recognition of the 5′ and 3′ splice sites: Exon binding sequences (EBS) 1–3 and intron binding sequences (IBS) 1–3 and δ–δ′ are noted. The EBS1 guide sequence (bold script) is contained within the apical loop of the ID3 stem–loop, the interaction of which with the IBS1 of exon 1 helps define the 5′ splice site. (B) The proposed secondary structure of the EBS1–IBS1 interaction involved in recognition of the 5′ splice site of the ai5γ group II intron. Watson-Crick base pairs identified in this study are marked with dashes and G•U wobble pairs with dots in black. The potential base pairs that were investigated here are denoted by gray dashes. Residues of the 5′ exon are shown in black. No pairing is formed between bases downstream from the 5′ splice site (noted by the wedge).
