Context-dependent structure formation of RNA hairpin motifs

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Abstract

Many functions of ribonucleic acid (RNA) rely on its ability to assume specific sequence-structure motifs. Packaging signals of some RNA viruses—hairpin motifs that interact with capsid proteins and drive self-assembly—are a prominent example. While interaction specificity demands the formation of stable motifs, they remain a small part of a much larger genomic RNA. An underexplored question is how the presence and composition of a flanking sequence around a motif interacts and interferes with its structure. Combining secondary and tertiary structure prediction, we study structural stability of 14 hairpin motifs from the RNA genome of MS2 bacteriophage and show that while some motif structures can be stable in any context, others require specific context provided by the genome. Our results demonstrate how important it is to consider RNA structure in its context and that changes in the flanking sequence of an RNA motif sometimes lead to drastic changes in its structure.

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