This proposal seeks to capitalize on the recent developments in RNA biochemistry to prepare purified RNA from a diverse range of systems in quantities sufficient for crystallographic studies. It focuses on three RNAs that span a broad range of sizes and structural motifs: dodecamer with non-canonical UU base pairs, a 30 nucleotide autolytic RNA, and a 160 nucleotide domain of the Tetrahymena intron. These RNAs will be examined with X-ray crystallography and several biochemical methods. Thermal denaturation, kinetic, and chemical protection studies will be used to refine understanding of the crystallographic structure. By integrating structural and biochemical results, Dr. Kundrot expects to obtain a better understanding of these RNA structures and how they function. %%% It has become increasingly apparent in the last decade that RNAs play many roles in a cell that are important in human health and biotechnology. The structures RNAs adopt are of manifest importance because they play central roles in the regulation of gene expression ranging from protein recognition sites to self- splicing active sites. The three-dimensional structure of RNA molecules must be determined if we are to understand how RNA can adopt stable folds and perform functions such as catalysis. Dr. Kundrot proposes to determine the structure of three RNA molecules: a self-cleaving RNA, an RNA with unusual base pairs, and a RNA folding domain that is more than twice as large as the largest RNA structure known today. These structures will provide with new insights into how RNA functions in cells and these insights will help in the development of drugs to improve human health and will open up new areas in biotechnology.
