RNA as a drug target: methods for biophysical characterization and screening

RNA folds into complex structures that can interact specifically with effector proteins. These interactions are essential for various biological functions. In order to discover small molecules that can affect important RNA–protein complexes, a thorough analysis of the thermodynamics and kinetics of RNA–protein binding is required. This can facilitate the formulation of high-throughput screening strategies and the development of structure–activity relationships for compound leads. In addition to traditional methods, such as filter binding, gel mobility shift assay and various fluorescence techniques, newer methods such as surface plasmon resonance and mass spectrometry are being used for the study of RNA–protein interactions.