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. Author manuscript; available in PMC: 2017 Jun 24.
Published in final edited form as: Q Rev Biophys. 2016 Jun 24;49:e10. doi: 10.1017/S003358351600007X

Figure 6.

Figure 6

RNA modifications by DMS (dimethyl sulfate), SHAPE reagents (Selective 2′-hydroxyl acylation analyzed by primer extension), and CMCT (1-cyclohexyl-(2-morpholinoehyl)carbodiimide metho-p-toluene). SHAPE reagents modify the 2′-hydroxyl on the sugar of all four nucleobases. SHAPE reagents include 1M7 (1-methyl-7-nitroisatoic anhydride), NMIA (N-methylisotoic anhydride), and NAI (2-methylnicotinic acid imidazolide). DMS modifies the N1 of A and the N3 of C as well as the N7 of G. CMCT modifies N3 of U and N1 of G. The chemical modifications (except N7 of G) can be detected immediately by RT followed by gel electrophoresis or high-throughput sequencing, and the enzymatic cleavages, which modify single- and double-stranded RNA, can be read out through gel electrophoresis or high-throughput sequencing.