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A new model of U2 RNA secondary structure has been developed by comparing U2 RNA sequences from distantly related trypanosomatids, which process their RNAs by trans-splicing, and U2 RNAs from cis-splicing organisms. The trypanosomatid U2 RNA retains structural similarity in important functional domains of cis-splicing U2 RNAs yet differs from previous consensus models in that only two helices, rather than three, can form in the stem-loop II region. This alteration eliminates the capacity for pseudoknot formation and produces a single-stranded region 3' to stem-loop II, which may be accessible for snRNP protein binding. Trypanosomatid U2 RNAs differ in the putative branchpoint recognition sequences, which completely diverge from the conserved GUAGUA consensus of cis-splicing organisms.

A new U2 RNA secondary structure provided by phylogenetic analysis of trypanosomatid U2 RNAs.