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Related Experiment Video

Updated: Apr 25, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA structural analysis by evolving SHAPE chemistry.

Robert C Spitale1, Ryan A Flynn, Eduardo A Torre

  • 1Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.

Wiley Interdisciplinary Reviews. RNA
|August 19, 2014
PubMed
Summary
This summary is machine-generated.

RNA structure is determined by its folding, not just its sequence. Selective 2'–hydroxyl acylation and primer extension (SHAPE) probes reveal RNA structure by targeting reactive 2'-hydroxyl groups, enabling genome-wide analysis.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genomics

Background:

  • RNA plays a crucial role in gene expression regulation, impacting cellular health and disease.
  • RNA's information content arises from both its linear sequence and complex 3D folding.
  • The reactivity of RNA's 2'-hydroxyl group is dependent on local nucleotide flexibility and base-pairing.

Purpose of the Study:

  • To describe the design and utilization of SHAPE probes for RNA structure characterization.
  • To highlight technological advances enabling parallel RNA structure probing using SHAPE chemistry.
  • To explore the potential of integrating SHAPE chemistry with deep sequencing for genome-wide RNA structure analysis.

Main Methods:

  • Development of reagents that modify RNA based on 2'-hydroxyl group reactivity.
  • Application of RNA SHAPE (selective 2'-hydroxyl acylation and primer extension) for structure probing.
  • Integration of SHAPE chemistry with deep sequencing for high-throughput analysis.

Main Results:

  • SHAPE probes effectively characterize RNA secondary and tertiary structures.
  • Advancements allow for parallel probing of multiple RNA molecules simultaneously.
  • The combination of SHAPE and deep sequencing facilitates genome-wide RNA structure mapping.

Conclusions:

  • SHAPE chemistry provides a powerful tool for understanding RNA structure and function.
  • Technological integration with genomics opens new avenues for studying RNA at a genome-wide scale.
  • This approach is essential for advancing our understanding of RNA's role in biological processes and disease.