1M7 (1-methyl-7-nitroisatoic anhydride) is the chemical most often used in the EteRNA lab SHAPE protocol to detect differences in configuration between the individual units of an RNA molecule's backbone. It has the potential to interact with one specific OH group of any backbone unit. The extent to which it actually interacts with each backbone unit yields information about the configuration of the atoms in that unit.
As a first approximation, the reactivity is thought to assesses local flexibility of the RNA backbone. In flexible regions (such as loops, bulges, and junctions), RNA adopts conformations that enhance the reaction. In stems (helical regions), the RNA backbone tends to adopt a conformation that protects the O2' atom from the reaction.