Using SHAPE-MaP to probe small molecule-RNA interactions

RNA is a regulator and catalyst of many cellular processes. Efforts to therapeutically harness RNA began with the discovery of myriad coding and non-coding RNAs and their versatile modes of action. However, due to its dynamic structure and the polar and repetitive nature of its surface, RNA presents a challenging target for drug design. For an RNA to be druggable, it must contain a motif that assumes a nearly fixed and unique conformation that a small molecule can recognize and bind consistently and with high affinity. Hence, reliable methods for determining the secondary and tertiary structures of RNA, and even the features and occupancy of potential drug binding sites are of utmost importance for the effective design of RNA-based therapeutics. Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) has emerged as such a method, by which RNA secondary structure can be probed at single-nucleotide resolution, under a variety of conditions, and in the presence of RNA-specific small-molecule ligands. In this review, we describe an in-depth protocol for using SHAPE-MaP to characterize RNA-small molecule interactions in cell culture (in cellulo). This method can be applied to transcripts of any size or abundance, and to determine the sites and affinities of small molecule binding, making it an essential and versatile tool for drug discovery.