Characterization of D135 group II intron ribozyme dimerization

Abstract

Group II introns are highly structured RNAs that carry out self-splicing reactions. The multiple turnover version of one of these introns, termed the D135 ribozyme, is derived from the mitochondrial aI5γ intron of Saccharomyces cerevisiae and is widely studied as a model RNA for group II intron folding. An important current goal is to probe global changes during its folding with or without DEAD-box chaperone proteins. My initial experiments to study global compaction using small angle X-ray scattering (SAXS) of D135 reveal rapid initial compaction. Unexpectedly, slower increases in Rg value and forward scattering were observed and shown to result from dimerization of the ribozyme. Dimerization was also observed with native electrophoretic mobility shift assays. Here, I have characterized the dimerization process at various conditions. Dimerization requires Mg2+, with similar concentration dependence as tertiary folding, and the dimer is efficiently disrupted by the ATP-dependent activity of DEAD-box proteins. Dimerization does not affect ribozyme catalysis, as both the monomer and the dimer are shown to be fully active. Further experiments showed that dimerization results from duplex formation by an artificial 3’ tail that has extensive self-complementarity, as the deletion of this tail ablates dimerization. Constructs lacking this artificial 3’ tail are likely to simplify further study of the folding process of this ribozyme.