Protocol for covalent RNA labeling by RiboLight dyes for detection by in-gel fluorescence and fluorescence microscopy

RNA abundance and localization provide key insights into cellular physiology and disease, making RNA a central target of basic and applied research. Here, we present a protocol for covalent labeling of RNA using RiboLight dyes for detection in gels and cells. We outline steps for cell culture, in vitro and cellular RNA labeling, sample purification, and visualization by in-gel fluorescence and fluorescence microscopy. This approach integrates readily into molecular and cellular biology workflows for RNA analysis. For complete details on the use and execution of this protocol, please refer to Shin et al.1