The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Accurate SHAPE-directed RNA structure determination
Open accessAbstract
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.
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Cites
Structure of the 30S ribosomal subunit
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Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
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Self-citationWilkinson, K. A., Merino, E. J., & Weeks, K. M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.249 · Cited by 780
Self-citationRegulation of translation via mRNA structure in prokaryotes and eukaryotes
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Cited by
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M. (2014) · Nature · doi:10.1038/nature12756 · Cited by 775
Targeting RNA structures with small molecules
Childs-Disney, J. L., Yang, X., Gibaut, Q. M. R., Tong, Y., Batey, R. T., & Disney, M. D. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00521-4 · Cited by 587
RNA SHAPE analysis in living cells
Spitale, R. C., Crisalli, P., Flynn, R. A., Torre, E. A., Kool, E. T., & Chang, H. Y. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1131 · Cited by 440
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Self-citationAccurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
Hajdin, C. E., Bellaousov, S., Huggins, W., Leonard, C. W., Mathews, D. H., & Weeks, K. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219988110 · Cited by 331
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Metadata
- Authors
- Deigan, K. E., Li, T. W., Mathews, D. H., & Weeks, K. M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2009-01-06
- Volume
- 106
- Issue
- 1
- Pages
- 97-102
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2071883352
- Cited by
- 696
- References
- 28
- FWCI
- 7.32
- Type
- journal article
- Language
- en
- Open access
- green
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