Comparison of SHAPE reagents for mapping RNA structures inside living cells

RNA. 2017 Feb;23(2):169-174. doi: 10.1261/rna.058784.116. Epub 2016 Nov 22.


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-N3 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-N3 give markedly greater signals with lower background than 1M7 for in vivo measurement of the RNA structurome.

Keywords: RNA structure; SHAPE.

Publication types

  • Comparative Study

MeSH terms

  • Acylation
  • Animals
  • Biological Assay / standards*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • High-Throughput Nucleotide Sequencing
  • Imidazoles / chemistry*
  • Indicators and Reagents
  • Mice
  • Mouse Embryonic Stem Cells / cytology
  • Mouse Embryonic Stem Cells / metabolism
  • Nitrosamines / chemistry
  • Nucleic Acid Conformation
  • Oxazines / chemistry*
  • Primary Cell Culture
  • RNA / chemistry*


  • Imidazoles
  • Indicators and Reagents
  • Nitrosamines
  • Oxazines
  • methylisoamylnitrosamine
  • RNA
  • isatoic anhydride