Helix 69, or H69, of the ribosome plays a key role in initiation and termination of translation. Small-molecule binding to this region could lead to inhibition of protein synthesis, an essential process throughout phylogeny. The H69 region of bacteria has been shown to bind certain peptides selectively, which may lead to new antimicrobials. The goal of this study is to identify compounds that bind to H69 by developing and using an optimized fluorescence-based assay. The assay uses TentaGel beads with bound synthetic peptides, biotinylated H69, and streptavidin-tagged quantum dots (Qdots). The interaction of H69 with the immobilized peptide is indicated through Qdot emission, which is visualized under a fluorescence microscope. The relative fluorescence value is quantified using Adobe software. In the future, the assay will be used to identify new binding ligands for H69.

Development of a fluorescence-based assay for RNA-ligand discovery

245th National Meeting (2013)

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