Applying DMS-MaPseq to Evaluate RNA-Ligand Binding

RNAs play pivotal roles in the cell due to their structures. RNA disfunction is implicated in many diseases, including cancers and neurodegenerative disorders, making RNA a critical drug target. However, the flexibility of RNA, its anionic nature, limited chemical diversity, and nonfunctional sites pose significant challenges in drug design. Furthermore, the chemical space of known RNA-binders is limited to non-drug-like compounds. Recent studies have suggested that RNA is a viable drug target as pockets have been found that are comparable to those found in druggable proteins and various assays have found drug-like compounds that bind to RNAs. These recent findings suggest the existence of a chemical space of drug-like RNA binders. To enable the development of RNA targeted therapeutics, this chemical space must be characterized. However, current methods to detect RNA-ligand interactions are either limited in their throughput or in the chemical scaffolds and targets that can be evaluated. This study aims to introduce the application of DMS-MaPseq as a high-throughput approach to evaluate a larger chemical space for RNA binding. Results demonstrate that titrations are able to robustly detect and characterize the binding events, while individual comparisons of standard and high concentration conditions are complicated by experimental variance.