My goal is to establish a vigorous, independent research program that focuses on the investigation of RNA-protein interactions and structure- function relationships in biological systems. The major function of transfer RNA (tRNA) molecules is to serve as a site of attachment for amino acids, which are then activated for use in protein synthesis. The high degree of specificity between tRNAs and aminoacyl-tRNA synthetases, the enzymes that catalyze this attachment, make these molecules excellent targets for studying the principles of protein-RNA interaction. Transfer RNA molecules are also used as primers by reverse transcriptases. These are enzymes in retroviruses that function to transcribe DNA from the retroviral RNA genome. A future direction of my lab will be to understand the interaction between HIV reverse transcriptase and human tRNA(Lys), the specific RNA primer for this viral enzyme. Briefly, the primary objective of this research is to address the question of how proline tRNA synthetase (ProRS) recognizes and interacts with its cognate tRNA substrate. We have already made progress in identifying the subset of nucleotides that mark a tRNA molecule for specific aminoacylation with proline. We have also demonstrated that a functional tRNA(Pro) molecule can be assembled by annealing together two oligonucleotides representing 3'- and 5'-fragments. The use of these """"""""annealed"""""""" substrates, prepared with a chemically-synthesized fragment, has facilitated the identification of RNA structural characteristics that are important for aminoacylation by ProRS. Novel applications of chemical RNA synthesis will enable the attachment of covalent probes at specific, internal positions of annealed tRNA substrates for use in cross-linking and fluorescence studies. In this way, protein structural motifs and specific amino acid residues in close contact with specific regions of tRNA(Pro) will be identified.
