A HIGH-THROUGHPUT FLUORESCENCE SCREEN TO MONITOR THE SPECIFIC BINDINGOF ANTAGONISTS TO RNA TARGETS

Since RNA molecules can form intricate three-dimensional structures, i t should be possible to design specific, high-affinity antagonists dir ected against these structures. To begin to explore the validity of th is possibility, high-throughput screening methods are required to assa y for RNA antagonists. A fluorescence quenching technique is described here in a 96-well plate format which is capable of screening chemical diversity libraries, A pyrene-containing aminoglycoside analog is use d to accurately monitor antagonist binding to a prokaryotic 16S rRNA A -site decoding region construct. This rRNA region comprises the natura l target for aminoglycoside antibiotics. The fluorescence technique re ported here should be generally adaptable to monitor the binding of st ructurally novel antagonists to any selected RNA target. (C) 1998 Acad emic Press.