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. Author manuscript; available in PMC: 2016 Jul 1.
Published in final edited form as: Neuron. 2015 Jul 1;87(1):28–46. doi: 10.1016/j.neuron.2015.06.012

Figure 4.

Figure 4

RNA structure prediction and chemical mapping. A) Phylogenetic analysis of three sequences highlighting conserved base paired regions (green) and mismatches (yellow). B) Two alternative structures predicted for sequence 3 by RNAstructure (Reuter and Mathews, 2010). Red arrows indicate locations of reactive hydroxyl groups identified by 2′-hydroxyl acylation and primer extension (SHAPE). Blue asterisks indicate A and C residues susceptible for methylation by dimethyl sulfate (DMS). C) Chemical reactions underlying SHAPE and DMS mapping. 1M7 is 1-methyl-7-nitroisatoic anhydride.