RNA-aminoglycoside antibiotic interactions: Fluorescence detection of binding and conformational change

A hammerhead ribozyme has been labeled with a fluorescein reporter dye which enables the nucleic acid to detect binding of small organic compounds such as neomycin. The fluorescent changes are associated with conformational changes in the RNA and can be used to determine the binding modes of the drugs. Abstract A fluorescent method for detecting small molecule-RNA interactions is reported. A hammerhead ribozyme was labeled with a fluorescein reported dye which enabled the RNA to detect binding of neomycin. This approach allowed the determination of neomycin binding modes in solution. Circular dichroism studies revealed that the fluorescent changes were associated with drug-induced