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RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE)
Abstract
The reactivity of an RNA ribose hydroxyl is shown to be exquisitely sensitive to local nucleotide flexibility because a conformationally constrained adjacent 3'-phosphodiester inhibits formation of the deprotonated, nucleophilic oxyanion form of the 2'-hydroxyl group. Reaction with an appropriate electrophile, N-methylisatoic anhydride, to form a 2'-O-adduct thus can be used to monitor local structure at every nucleotide in an RNA. We develop a quantitative approach involving Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) to map the structure of and to distinguish fine differences in structure for tRNAAsp transcripts at single nucleotide resolution. Modest extensions of the SHAPE approach will allow RNA structure to be monitored comprehensively and at single nucleotide resolution for RNAs of arbitrary sequence and structural complexity and under diverse solution environments.
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Citations
Cited by
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Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast
Kudla, G., Granneman, S., Hahn, D., Beggs, J. D., & Tollervey, D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017386108 · Cited by 308
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Keane, S. C., Heng, X., Lu, K., Kharytonchyk, S., Ramakrishnan, V., Carter, G., Barton, S., Hosic, A., Florwick, A., Santos, J., et al. (2015) · Science · doi:10.1126/science.aaa9266 · Cited by 278
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Serganov, A., & Patel, D. J. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-101211-113224 · Cited by 160
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Bowler, F. R., Chan, C. K. W., Duffy, C. D., Gerland, B., Islam, S., Powner, M. W., Sutherland, J. D., & Xu, J. (2013) · Nature Chemistry · doi:10.1038/nchem.1626 · Cited by 108
Metadata
- Authors
- Merino, E. J., Wilkinson, K. A., Coughlan, J. L., & Weeks, K. M.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-03-01
- Volume
- 127
- Issue
- 12
- Pages
- 4223-4231
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2120974004
- Cited by
- 796
- References
- 0
- FWCI
- 6.34
- Type
- journal article
- Language
- en
- Open access
- closed
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- Merino, E. J., Wilkinson, K. A., Coughlan, J. L., & Weeks, K. M. (2005). RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE). Journal of the American Chemical Society. https://doi.org/10.1021/ja043822v
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