Simply turn off a virus: Scientists develop new method for detailed investigation of functional RNA elements

For a long time molecular biologists believed that RNA is a short-lived storage medium. DNA (deoxyribonucleic acid), the blueprint of every living thing, is transcribed into RNA, which in turn is translated into protein, which then takes over certain functions in the body. Following the discovery of non-coding RNA, it has become more and more recognized that different types of RNA are functionally active and regulate almost all aspects of cellular function. At the molecular level, RNA can bind DNA to deactivate gene segments, bind other RNA or it can bind proteins, activating or deactivating them. In addition, RNA can itself be enzymatically active, i.e., it can catalyze biochemical reactions.

The research group developed the molecular biology method MIME (Mutational Interference Mapping Experiment) to investigate the interaction of RNA with its respective interaction partners in detail. The scientists chose an evolutionary approach: The RNA to be analyzed is randomly mutated, so that a pool of billions of randomly mutated RNA is produced. An interaction partner such as a protein is added to this pool so that selection pressure with respect to the interaction arises. The resulting pools of RNA, separated according to functionality (e.g., protein-binding vs. non-binding) are sequenced with next generation technologies. This way the researchers obtain data for each type of mutation as well as precise mutation frequencies at any position of the RNA. Through mathematical and statistical calculations developed by bioinformatics researcher Max von Kleist, the functional consequence of every possible mutation can be quantified. The researchers can also determine which part and structural configuration of the RNA is responsible for the investigated function.

The MIME method is groundbreaking in the study of viral replication. Many of the most threatening diseases are transmitted by so-called RNA viruses, such as HIV, influenza, and hepatitis C. What they have in common is that the genome does not consist of DNA, but RNA. Using MIME, scientists can determine how the genetic material of a virus is incorporated into nascent virions at the end of its reproductive cycle. This has great significance for medical practice: If it was possible to stop this process, e.g., by introducing therapeutic (e.g. complementary) RNA, the virus could be rendered harmless.

Currently, many RNA-based therapies are under investigation worldwide. The MIME method can make a significant contribution to this research by helping to identify the appropriate RNA segments. The method also provides information about which mutations are tolerated by the virus and which not, a factor that is useful for the design of therapeutic RNA, i.e. by preventing viruses from developing resistance.