Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. 2017. Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA (New York, N.Y.). 23(2):169-174. Pubmed: 27879433 DOI:10.1261/rna.058784.116


Recent advances in SHAPE technology have converted the classic primer extension method to next-generation sequencing platforms, allowing transcriptome-level analysis of RNA secondary structure. In particular, icSHAPE and SHAPE-MaP, using NAI-N and 1M7 reagents, respectively, are methods that claim to measure in vivo structure with high-throughput sequencing. However, these compounds have not been compared on an unbiased, raw-signal level. Here, we directly compare several in vivo SHAPE acylation reagents using the simple primer extension assay. We conclude that while multiple SHAPE technologies are effective at measuring purified RNAs in vitro, acylimidazole reagents NAI and NAI-N give markedly greater signals with lower background than 1M7 for in vivo measurement of the RNA structurome.
© 2017 Lee et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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Ryan Flynn’s laboratory is focused on the exploration and discovery of how biopolymers like RNA and glycans work together to control cellular processes in the context of human disease.

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