RNA is one of the most important molecules along with DNA and proteins for the regulation of cells’ life. Several types of RNA molecules participate in the process of gene expression and for their role is fundamental the structure they assume. Differently from DNA, RNA can fold into intricate structures at secondary or tertiary level. A class of RNA of great importance is the non-coding RNAs. Knowing the structure of these molecules leads to understand their function and how they influence the expression of the genes. Nowadays it is not possible to exactly determinate in vivo the secondary structures of the molecules.