Application of a fluorescently labeled trans-acting antigenomic HDV ribozyme to monitor antibiotic–RNA interactions

Abstract

In order to determine if a fluorescently labeled trans-acting antigenomic HDV ribozyme can be used to monitor antibiotic–RNA interactions, several parameters that can influence assay sensitivity and reproducibility were tested and optimized. Applicability of the assay for rapid screening of antibiotics targeting the HDV ribozyme was shown by using selected antibiotics and their complexes with copper(II) ions, also at various pH conditions. Potential antibiotics which are intrinsically fluorescent or intercalated can also be tested. The assay was very sensitive, since a single nucleotide mutation of the ribozyme target in the J4/2 region influencing the RNA–antibiotic interaction was detected. Consequently, the fluorophore-labeled HDV ribozyme is a good model for the rapid screening of antibiotics, and possibly, also for other low-molecular-weight compounds which target RNA molecules.