Riboswitches interact with small molecules, such as metabolites, to change the secondary structure of the RNA molecule. This is used to regulate protein expression, post-translationally.
Some RNA molecules have a secondary structure that occludes the Shine-Dalgarno sequence, preventing ribosome binding until a metabolite is present. This could be ATP binding, controlling the expression of a biosynthetic pathway that requires a certain concentration of ATP to be present in the cell. The reverse can also be true, only allowing translation when a metabolite’s concentration is low (such as amino acids, by detecting the concentration of charged tRNAs).
tRNAs are able to interact with the mRNA transcript through the anticodon. This binding causes changes in the secondary structure of the RNA, depending on whether the tRNA molecule is charged with an amino acid.
Small molecules are also able to interact directly with the nucleic acid. This can also cause changes in the secondary structure of the RNA. The molecule binds to the aptamer domain of the RNA, causing a conformational change through the switching sequence to the expression platform. This change can be caused by any metabolite that is able to bind specifically to the RNA’s aptamer domain.