Methods and kits for discovery of RNA-binding antimicrobials

A kit for determining whether a test compound binds to a target RNA, the kit comprising (a) a target RNA labelled with a donor group or an acceptor group and (b) an antimicrobial labelled with a group that is acceptor or donor to the label on said target RNA, wherein the antimicrobial and the target RNA bind to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer and/or quenching.

A method for determining the presence in a biological sample of a compound that binds to a target RNA molecule, comprising

• (a) contacting the sample with a pair of indicator molecules comprising an antimicrobial labelled with a donor group or an acceptor group and the target RNA labelled with a group that is acceptor or donor to the label on said antimicrobial, wherein the pair bind to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer and/or quenching to take place;
• and
• (b) measuring fluorescence of the target RNA and the antimicrobial in said step (a) to obtain a fluorescence value and comparing this value to fluorescence of a standard, wherein a difference in said value and the fluorescence of said standard is an indication of the presence in a biological sample of a compound that binds to said target RNA.