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

Aminoglycosides: Perspectives on Mechanisms of Action and Resistance and Strategies to Counter Resistance

“…In general, aminoglycosides that share structural features with paromomycin bind to rRNA similarly (13). However, different aminoglycoside antibiotics appear to bind to the same binding site in more than one conformation (28). In essence, the conformation of the aminoglycoside that does bind to RNA must satisfy the electronic and steric constraints of the binding site.…”

Fluorescence resonance energy transfer studies of aminoglycoside binding to a T box antiterminator RNA

“…2 Various fluorescent measurement techniques have been employed to study RNA-small molecule interactions. [12][13][14][15][16][17] In preliminary studies of the T box antiterminator RNA, a simple fluorescence-quenching assay was employed to measure the binding of the aminoglycosides with a 5 0 -fluorescein-labeled AM1A antiterminator model. There was no discernable change in the fluorescence spectra of the labeled RNA (data not shown).…”

Binding of an aminoacridine derivative to a GAAA RNA tetraloop

“…There are two general methods to enable fluorescence studies when the small molecule is not fluorescent: a competition experiment can be performed to monitor the displacement of a fluorescent molecule known to bind the target RNA by the nonfluorescent molecule; 42,43 or a direct measurement can be made by monitoring the change in fluorescence of a fluorophore incorporated into the target RNA upon addition of the nonfluorescent molecule. 44,45 Because no GAAA tetraloop ligands were known, we chose to label the GAAA tetraloop by substituting 2-aminopurine for A8. A normal titration was performed in which the fluorescence intensity of 2-aminopurine was monitored as a function of increasing concentrations of neomycin or kanamycin.…”