Accurate SHAPE-directed RNA structure determination

doi:10.1073/pnas.0806929106

Accurate SHAPE-directed RNA structure determination

^aDepartment of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290; and
^bDepartment of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642

Edited by Ignacio Tinoco, Jr., University of California, Berkeley, CA, and approved October 30, 2008 (received for review July 16, 2008)

Abstract

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 minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis.

Footnotes

¹To whom correspondence may be addressed. E-mail: weeks{at}unc.edu or david_mathews{at}urmc.rochester.edu
Author contributions: K.E.D., T.W.L., D.H.M., and K.M.W. designed research; K.E.D., T.W.L., and D.H.M. performed research; K.E.D., T.W.L., D.H.M., and K.M.W. analyzed data; and K.E.D., D.H.M., and K.M.W. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/cgi/content/full/0806929106/DCSupplemental.