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Sequence requirements for branch formation in a group II self-splicing intron.

Evidence is presented for the existence of a specific intron-intron interaction, necessary for the formation of the branched product in the self-splicing reaction of a group II yeast mitochondrial intron. Trans-splicing reactions involving two RNA molecules (5' exon with covalently linked regions of intron and intron with covalently linked 3' exon) show that the presence of portions of intron domain I on the 5' molecule is necessary for the formation of branched products which are not seen with shorter 5' molecules. Modification/interference reactions show regions necesary for branch-formation and support a major role for specific regions of intron domain I. Further experiments, utilizing a truncated 3' molecule that is missing the conserved branchpoint nucleotide, indicate that domain VI may be required for a successful domain I interaction. A model for the formation of a proper branched structure includes implications for both cis and trans configurations.