Ribonucleic acids (RNAs) are biopolymers that play key roles in many processes crucial for the life of cells. Functions of RNAs are generally mediated by their specific interactions with proteins and ribonucleoproteins (supramolecular RNA-protein complexes) that take place within complexes of RNA ligands with proteins or ribonucleoproteins. These interactions are defined by the molecular environment of the RNA ligand in the complex. A beneficial approach for studying such complexes involves site-directed cross-linking: RNA derivatives that contain chemically reactive groups form covalent bonds (cross-links) with those structural elements of the protein or ribonucleoprotein that neighbor the RNA ligand. Such RNA derivatives have been successfully used to study the interaction of messenger RNA (mRNA) with the protein synthesis machinery. By applying this approach to studies of the protein translation machinery of higher organisms, chemically reactive RNA derivatives have provided unique information that could not have been obtained by other approaches to date. This article presents a brief review of the types of RNA derivatives used as mRNA analogs, and their structures and synthesis, together with methods for identification of cross-linking targets. Furthermore, we summarize current data on mRNA interactions occurring during the course of protein synthesis in higher organisms.