My co-authors and I have devised a simple, low-cost method to modify RNA with sulfinate salts that can directly add almost any desired functional group under mild conditions. Existing methods of RNA modification have relatively limited applicability due to constraints on the size of the RNA and the lack of diversity of possible modifications. This chemistry modifies the Hoogsteen edge of nucleobases and is done as a single pot reaction. It can be applied to RNA or DNA of any size, as well as to individual nucleotides. Sulfinate salts can modify RNA with a broad range of functional groups, such as fluorophores, biotin and medicinally relevant small molecules such as trifluoromethyl groups. This methodology enables the exploration of diverse chemical groups on RNA that can potentially confer protection from nucleases, allow for efficient delivery of nucleic acids into cells, and act as new tools for the investigation of nucleic acid structure and function.
Prior to working on the chemical modification of RNA, I attempted to solve the structure of a viroid using cryo-electron microscopy (cryo-EM) and x-ray crystallography. Viroids are infectious RNAs that target plants, including important food crops such as potatoes, apples and avocados. They are 240 to 400 nucleotides long, single stranded, covalently closed circular RNAs. Viroids, incredibly, do not encode protein and have no DNA replication intermediate. Of the secondary structures that have been experimentally determined, two are predicted to fold into higher order tertiary structures: the peach latent mosaic viroid (PLMVd) and the chrysanthemum chlorotic mottle viroid (CChMVd). Biochemical evidence suggests that these tertiary interactions are essential for infectivity. Many attempts were made to solve a viroid structure with both x-ray crystallography and cryo-EM, but I was ultimately unsuccessful due to the viroid’s persistent aggregation.