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Site-specific RNase E cleavage of oligonucleotides and inhibition by stem–loops

Abstract

THE enzyme RNase E (ref. 1) cuts RNA at specific sites within single-stranded segments2–6. The role of adjacent regions of secondary structure in such cleavages is controversial7–10. Here we report that 10–13-nucleotide oligomers lacking any stem–loop but containing the RNase E-cleaved sequence of RNA 11–13, the anti-sense represser of replication of ColEl-type plasmids, are cut at the same phosphodiester bond as, and 20 times more efficiently than, RNA I. These findings indicate that, contrary to previous proposals8,9, stem–loops do not serve as entry sites for RNase E, but instead limit cleavage at potentially susceptible sites. Cleavage was reduced further by mutations in a nonadjacent stem-loop, suggesting that distant conformational changes can also affect enzyme access. Modulation of RNase E cleavages by stem-loop regions and to a lesser extent by higher-order structure may explain why this enzyme, which does not have stringent sequence specificity6,12,13, cleaves complex RNAs at a limited number of sites.

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McDowall, K., Kaberdin, V., Wu, SW. et al. Site-specific RNase E cleavage of oligonucleotides and inhibition by stem–loops. Nature 374, 287–290 (1995). https://doi.org/10.1038/374287a0

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