Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries

The large-scale analysis of small-molecule binding to diverse RNA structures is key to understanding the required interaction properties and selectivity for developing RNA-binding molecules toward RNA-targeted therapies. Here, we report a new system for performing the large-scale analysis of small molecule–RNA interactions using a multiplexed pull-down assay with RNA structure libraries. The system profiled the RNA-binding landscapes of G-clamp and thiazole orange derivatives, which recognizes an unpaired guanine base and are good probes for fluorescent indicator displacement (FID) assays, respectively. We discuss the binding preferences of these molecules based on their large-scale affinity profiles. In addition, we selected combinations of fluorescent indicators and different ranks of RNA based on the information and screened for RNA-binding molecules using FID. RNAs with high- and intermediate-rank RNA provided reliable results. Our system provides fundamental information about small molecule–RNA interactions and facilitates the discovery of novel RNA-binding molecules. Targeting RNA with small molecules represents an attractive medicinal approach, and profiling the small molecule-binding landscapes of various types of RNA structures is critical. Here, the authors develop a large-scale approach for investigating small molecule-RNA structure interaction profiles using a multiplexed pull-down assay with various RNA structure libraries, and validate the assay using G-clamp and thiazole orange derivatives.