A biophysical assay for RNA based resistance

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PROJECT SUMMARY The world is rapidly heading towards a pre-1940's scenario when it comes to fighting infectious disease. Antimicrobial resistance is a growing problem on a global scale, greatly hampering our abilities to quell worldwide epidemics such as tuberculosis and malaria, as well as the simple staphylococcus infection. The proposed project is significant because unless innovative strategies are developed to produce robust and effective new classes of antibiotics, health care costs will continue to climb and we will completely lose our ability to combat even the most common infection. Current antibiotic treatments originated predominantly from natural products produced by fungi and bacteria that were able to inhibit the growth of other organisms, usually by inhibiting cell wall synthesis or maintenance or by inhibiting protein synthesis. Since penicillin was first isolated by Fleming in 1929, most of the subsequent generations of antibiotics remain very similar to the original natural products, with functional groups modified to increase their activity across a broader range of pathogens and decrease their side effect profiles. Oxazolidones, glycopeptides, b-lactams, and quinolones show some promise for the future, but gram-negative bacterial infections still remain problematic. Nucleic acids are promising avenues for drug design, both as therapeutics and as targets. Here we propose an innovative plan for identification of a novel class of ligands that are specific for an RNA element that is an important factor in the antibiotic resistance in dozens of pathogenic bacterial strains, and we propose a biophysical screening assay for identifying such ligands. First, as outlined in Specific Aim 1, we will characterize a model nucleic acid domain that has been synthesized commercially with modifications allowing structural and dynamic properties of this molecule in bulk solution. We will then synthesize sequence-specific RNA binding ligands and screen these targeted library of conjugates for sequence-specifically binding and inhibiting the target nucleic acid to (Specific Aim 2). A successful application of the approach will allow us to silence the resistance pathway for a class of widely used antibiotics-the aminoglycosides.