Structure-function mapping of large intracellular viral RNA.

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This research program will study the tridimensional structure of a basic molecule of life, namely ribonucleic acid (RNA). Until recently, a type of RNA known as "messenger RNA" was thought to have just a passive role, notably as a template for the conversion of genetic information into protein. There is recent evidence suggesting that certain messenger RNA molecules exhibit structural patterns that can control whether genes are silent or expressed. Little is known, however, on the structure of RNA as it exists inside living cells. While computer models are commonly used to predict the shapes of RNA molecules, it is difficult to achieve a high degree of accuracy using computer modeling alone. This is further complicated by the fact that intracellular RNA is encased within a protein coat, and does not exist as a free-floating strand. Our research program aims to gain a better understanding of the structure of intracellular RNA by using the RNA genome of the hepatitis C virus (which mimics messenger RNA) as a model system and examining how this RNA exists inside a living cell. We have developed a unique approach to probe complex structures formed by the folding of RNA inside the cell. The first objective of our research program is to map the location of loop-shaped helical structures that may form as part of the natural folding process of the intracellular genome of the hepatitis C virus. Our second objective is to examine how distant parts of this genome can perfectly align inside cells and, consequently, cause the viral genome to fold into a large circular molecule. By introducing mutations into the RNA that disrupt these alignments, we should be able to determine whether such alignments are important for specific functions. An understanding of the complex intracellular folding within the RNA genome of the hepatitis C virus would constitute a significant step forward in our knowledge of RNA, which should lead to a better understanding of how genes are expressed. This knowledge is the basis for the development of new products and technologies in genetic engineering.