Accurate SHAPE-directed RNA structure determination

Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure-function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy…

• NS
  National Science Foundation

  Award: 0416941
• AA
  Arnold and Mabel Beckman Foundation
• FC
  Frances C. and William P. Smallwood Foundation
• NI
  National Institutes of Health

  Awards: AI068462, GM076485
• UO
  University of North Carolina at Chapel Hill