Guide RNAs in kinetoplastid mitochondria have a nonencoded 3' oligo(U) tail involved in recognition of the preedited region.

Maxicircle-encoded guide RNAs (gRNAs) for cytochrome b and maxicircle unidentified reading frames 2 and 3 (MURF2 and MURF3) were isolated by hybrid selection and sequenced. All three gRNAs contained nonencoded 3' oligo(U) tails 5-24 nucleotides in length, with a mean length of approximately 15 nucleotides. Secondary structure calculations indicate a functional role of the 3' oligo(U) tail in stabilizing the initial hybrid formed between the gRNA and the preedited mRNA, and allowed the identification of potential mRNA recognition sites for an editing complex. In addition, isolated MURF2 gRNA-II could be 5' capped with [alpha-32P]-GTP and guanylyltransferase, suggesting that at least some gRNAs represent primary transcripts.