Grant: Operating Grant

Proteins are assembled in the cell based on the genetic code, but this code can be altered by shifting the frame in which it is read. In viruses like HIV, SARS, and many others, such recoding is programmed into the genome using specific structures in the RNA message. Using drugs to alter this recoding presents an attractive approach to develop anti-viral therapies which is being actively pursued. However, the molecular mechanism by which the recoding works remains controversial, hindering efforts at drug discovery. We recently discovered that the dynamical properties of RNA structures play an under-appreciated role in recoding of the genome, by using laser tweezers to manipulate RNA structures mechanically and probe their dynamics. We will extend these initial studies to investigate how recoding mechanisms depend on the dynamics of the structures in messenger RNA that stimulate the recoding. Our goal is to understand what properties of the RNA determine the efficiency of recoding, and how the RNA interacts with the protein synthesis machinery to trigger a recoding event. We will study single RNA molecules with structures that stimulate recoding, taken from a variety of viruses including HIV and SARS, not only in isolation, but also in the presence of the ribosomes which synthesize proteins. We will also investigate the effects of putative drugs that have been found to alter recoding efficiency and reduce infectivity, to determine their mechanism of action. We expect this work to lead to improved understanding of recoding mechanisms and the discovery of new targets for anti-viral drug development.