Recent advances in invitro selection and evolution techniques have identified novel RNA secondary structures selected from random RNA libraries that target immobilized ligands with high affinity and specificity. The major focus of this application is to structurally characterize ligand-RNA aptamer complexes at high resolution through a combination of NMR and molecular dynamics techniques on uniformly 13C, 15N-labelled RNA. These efforts will be extended to the measurement of base pair opening lifetimes and the identification of potential long lived hydration sites in these ligand-RNA aptamer systems. Preliminary NMR data are presented on RNA aptamers complexed to flavin mononucleotide, adenosine triphosphate and the aminoglycoside antibiotic tobramycin that exhibit extremely well resolved spectra and are amenable to structural characterization in solution. The consensus RNA sequences targeted by these and related ligands are located within internal bulges and hairpin loops, as well as pseudoknots and G-quadruplexes. These are challenging times in the RNA aptamer field where, despite the exponential growth in publications, not a single structure has been reported that defines the principles associated with RNA folding and molecular recognition. This application outlines a structural program on a range of RNA aptamers bound to cofactors and therapeutic agents with the emphasis on the identification and characterization of novel RNA three dimensional folds and aimed towards an understanding of the molecular basis for the striking selectively associated with target recognition.
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