Detection of metabolites in real time and in whole cells requires effective molecular sensors. In this regard, fluorogenic light-up RNAs have recently become important tools for small-molecule detection in cells. However, the construction of light-up RNA sensors is an arduous task that requires structural knowledge of both the sensor and reporter RNA. De novo strategies for selecting sensors from RNA libraries are limited and are mostly restricted to known aptamers and riboswitches. Here, we provide a solution to this problem by developing a capture-SELEX variant that allows the obtained libraries and aptamers to be linked to fluorogenic RNAs in a modular and allosteric manner. The approach is generally applicable and allows for rapid modular allosteric assembly with green- or red-shifted fluorogenic RNAs.
Keywords: broccoli aptamer; capture-SELEX; fluorogenic RNA sensor; light-up RNA aptamers; thiamine pyrophosphate.