Linking the branchpoint helix to a newly found receptor allows lariat formation by a group II intron

Abstract

Like spliceosomal introns, the ribozyme-containing group II introns are excised as branched, lariat structures: a 2-2-"5-2 bond is created between the first nucleotide of the intron and an adenosine in domain VI, a component which is missing from available crystal structures of the ribozyme. Comparative sequence analysis, modelling and nucleotide substitutions point to the existence, and probable location, of a specific RNA receptor for the section of domain VI that lies just distal to the branchpoint adenosine. By designing oligonucleotides that tether domain VI to this novel binding site, we have been able to specifically activate lariat formation in an engineered, defective group II ribozyme. The location of the newly identified receptor implies that prior to exon ligation, the distal part of domain VI undergoes a major translocation, which can now be brought under control by the system of anchoring oligonucleotides we have developed. Interestingly, these oligonucleotides, which link the branchpoint helix and the binding site for intron nucleotides 3-"4, may be viewed as counterparts of U2-"U6 helix III in the spliceosome. © 2011 European Molecular Biology Organization.