THE LEPTOMONAS-COLLOSOMA SPLICED LEADER RNA CAN SWITCH BETWEEN 2 ALTERNATE STRUCTURAL FORMS

We have used a combination of physical and molecular biological techni ques to examine the structure of Leptomonas collosoma spliced leader R NA. We confirm the general features of the previously proposed structu re for the 3' half of the RNA, in which a single-stranded region is fl anked by two stem loops. However, we find that the 5' half of the RNA, which contains the splice site, has two competing secondary structure s which differ only slightly in stability and which can interconvert o n a fast (< 1 s) time scale. In the favored conformation, a stable hai rpin helix is augmented by conserved complementarity between the splic e site and the 5' end of the SL RNA. This putative helix has anomalous nuclease sensitivity and thermal stability features, suggesting that it is probably coupled by unknown tertiary interactions to other nucle otides in the 5' half-molecule. The structure offers intriguing parall els with RNA-RNA interactions in the mammalian splicing system.