RNA electrophoretic mobility shift assay using a fluorescent DNA sequencer

The RNA electrophoretic mobility shift assay is a simple and rapid method for visualizing the existence of specific RNA-protein interaction. We have developed a useful method for the detection of mRNA binding proteins using non-radioactive RNA. In this method, RNA was prepared by in vitro transcription using Texas Red-labeled nucleotides. The synthesized RNA from chicken αA-globin 3′-UTR region, which has been shown to bind various proteins as α-complex, was detected with an automatic fluorescent DNA sequencer. This method has higher resolution than the conventional method using slab gels and is both safer and provides results rapidly due to the use of fluorescence detection.