From Eterna Wiki

DMS stands for dimethyl sulfate. Basically DMS is footprinting or fingerprinting of the RNA secondary structure. It is a chemical check of which bases are paired as they should be and which are not. Rhiju describes it as doing the following: DMS reacts only with unpaired A and C nucleotides. Nando explains, "DMS works by binding the Watson-Crick edge". As Brourd added it 1.5 - 3 days to complete.

The abstract of this science paper does a good job of explaining what DMS is.