The differential SHAPE experiment uses three reagents, the workhorse 1M7 (1-methyl-7-nitroisatoic anhydride) reagent to measure local nucleotide dynamics, plus NMIA and 1M6 (N-methylisatoic anhydride and 1-methyl-6-nitroisatoic anhydride) which together detect higher-order and noncanonical interactions. Among other uses, the resulting three-reagent SHAPE experiment makes possible very accurate modeling of RNA secondary structure.
G.M. Rice, S. Busan, F. Karabiber, O.V. Favorov and K.M. Weeks, SHAPE analysis of small RNAs and riboswitches. Methods Enzymol. 549, 165-187 (2014). link pdf
G.M. Rice, C.W. Leonard and K.M. Weeks, RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA 20, 846-854 (2014). link pdf