P4-P6 from Tetrahymena group I intron bound to Fab antibody
Our group is broadly interested in the chemistry and biochemistry of nucleic acids with particular emphasis on RNA and RNA catalysis. The laboratory integrates areas of organic chemistry, physical chemistry, enzymology and molecular biology to gain a fundamental understanding of nucleic acid structure and mechanisms of RNA catalysis. Using the principles and techniques of organic chemistry and molecular biology, we manipulate the structure of RNA molecules at precise locations in ways that are designed to answer very specific questions about biological function.
We employ these approaches toward gaining a fundamental understanding of the role that divalent metal ions play in phosphoryl transfer reactions that occur during RNA splicing, an important step in genetic expression. One experimental system that we are using to address these issues is the self-splicing intervening sequence RNA of the ciliated protozoan Tetrahymena. Shortened forms of this RNA can act as enzymes, catalyzing the sequence specific cleavage of RNA and DNA substrates with multiple turnover. We have used sulfur substitution of the oxygen substituents on the phosphoryl group undergoing transfer to reveal the transition state interactions between the ribozyme and the scissile phosphate.
The Piccirilli lab, in collaboration with the Kossiakoff and Koide labs, has developed new technology to derive RNA-specific antibodies using a synthetic phage display libraries. One application of these antibodies is for RNA crystallography, an extremely challenging area of research. While there are currently over 40,000 protein structures solved in the Protein DataBank, fewer than 1,000 RNA structures have been solved. Using a chaperon, such as a nucleic acid binding antibody fragment (Fab), can help overcome some of these challenged by promoting crystal formation.
Another area of interest is the development of new methods and model systems for studying RNA molecules. For example, we have recently designed a series of nucleoside analogues in which the 2′-beta-hydrogen atom is replaced by CH3, CH2F, CHF 2, or CF 3 . These analogues provide a systematic way to perturb the acidity of the 2′-OH group, thereby allowing us to probe the all important role of this functional group in RNA mediated biological processes.
See the News page for our most recent work.