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Most methods for labeling RNA make use of RNA aptamers attached to RNA. These aptamers are then labeled with a cognate RNA-binding protein that is fused with the fluorescent protein. Several years ago we modified this aptamer-based approach by introducing protein complementation (PC). In this approach the fluorescent protein is split and non-fluorescent until it is bound to RNA. Application of PC allowed to reduce the fluorescent background and thus to increase sensitivity of RNA detection (Valencia-Burton et al., 2007, 2009). To overcome another important limitation of the aptamer-based RNA labeling-the necessity to modify RNA by aptamer tagging-we combined protein complementation with the split aptamer approach (Toran et al., 2014, see Fig). In this method the cells are programmed to express two RNA probes that contain split aptamer sequences flanked with the anti-sense arms. Both RNA probes …