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Updated: Jan 21, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Physical and Functional Analysis of Viral RNA Genomes by SHAPE
Mark A Boerneke1, Jeffrey E Ehrhardt1, Kevin M Weeks1
1Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; email: mboernek@email.unc.edu, ejeffrey@ad.unc.edu, weeks@unc.edu.
Abstract:
RNA viruses encode the information required to usurp cellular metabolism and gene regulation and to enable their own replication in two ways: in the linear sequence of their RNA genomes and in higher-order structures that form when the genomic RNA strand folds back on itself. Application of high-resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes has identified numerous new regulatory elements, defined new principles by which viral RNAs interact with the cellular host and evade host immune responses, and revealed relationships between virus evolution and RNA structure. This review summarizes our current understanding of genome structure-function interrelationships for RNA viruses, as informed by SHAPE structure probing, and outlines opportunities for future studies.
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