Rare RNA sequences capable of binding specific ligands can be isolated from large pools of random sequence molecules. Such ligand binding sequences, known as aptamers, may be enriched by affinity chromatography, and isolated by repeated cycles of enrichment and amplification. The P.I. will characterize several recently isolated aptamers with specificity for common metabolic substrates and cofactors. He will also isolate new aptamers to additional substrates and cofactors in order to explore the affinity and specificity with which chemically diverse ligands can be bound by RNA structures. He will study the nature of the binding sites and the types of interactions that are important for binding by chemical and molecular biological means. Structural studies will be pursued in collaboration with NMR and X-ray crystallography labs. As functional RNA sequences are isolated, the P.I. will search for occurrences of these structures in the sequence databases for possible examples of the use of these structures in biology; the significance of any such occurrences will be tested genetically. This work will have significant implications for a number of areas of research. The isolation of RNA structures capable of binding all major classes of biological substrates and cofactors increases the plausibility of models in which the evolution of intermediary metabolism occurred at the time of the RNA world. Studies of the directed evolution of RNA structures from one binding specificity to another will improve our understanding of the evolutionary flexibility of RNA, and will eventually allow a comparison of the abilities of nucleic acids and proteins to evolve new functions, including the development of new catalysts. The solution of new RNA structures should lead to a better understanding of the principles of nucleic acid folding. Finally, the technology developed in the course of this work may have applications in the areas of molecular recognition, diagnostics, biosensors, and pharmaceuticals. %%% Many scientists now believe that RNA enzymes played an important role in the origin and early evolution of life. For this to be true, RNA molecules would have to be able to speed up a wide range of different chemical reactions; this in turn implies that RNA molecules would have to be able to bind tightly to a variety of different small molecules. This lab has recently been able to show that RNA's can in fact form very specific small molecule binding sites. They started with a large pool of random RNA sequences, and then used a laboratory version of Darwinian evolution to select for the rare RNA sequences capable of binding specific target molecules. Several o of these RNA's will be characterized to try to understand how they recognize their targets. The lab also plans to try to understand how they recognize their targets. The lab also plans to search for possible examples of the use of such RNA structures in biology. This work will improve our understanding of how RNA carries out its varied structural and catalytic roles in biology, and may lead to applications in the areas of molecular recognition, diagnostics, biosensors, and pharmaceuticals.
