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

RNA folds into complex structures that can interact specifically with effec tor proteins. These interactions are essential for various biological funct ions. In order to discover small molecules that can affect important RNA-pr otein complexes, a thorough analysis of the thermodynamics and kinetics of RNA-protein binding is required. This can facilitate the formulation of hig h-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 techn iques, newer methods such as surface plasmon resonance and mass spectrometr y are being used for the study of RNA-protein interactions.