Surface Plasmon Resonance Study of RNA–Aminoglycoside Interactions

Abstract

An increasing number of small molecules with different structures have been discovered that bind to RNA. With the advanced techniques available to elucidate RNA structures and probe RNA–small molecule interactions, the underlying recognition principles regarding molecular details are just beginning to be revealed. For rational design of selective RNA binders, detailed knowledge of structure–affinity relationships between RNA and small molecules is required, as well as analysis of the binding specificity of various RNA sequences. Several methods have been used to investigate the binding between RNA and small molecules. Surface plasmon resonance (SPR) biosensor has been used to measure RNA–small molecule interactions and provides real-time monitoring without a labeling requirement. Although the SPR-based method has been applied to monitor macromolecular interactions, only more recently, with improved instrument detection accuracy, bindings between small molecules and macromolecules can be successfully monitored by SPR. This chapter focuses on describing procedures performed in the SPR binding assay, using aminoglycoside–bacterial ribosome 16S A-site binding as an example. The methods of data analysis to derive the equilibrium constant and binding stoichiometry are also discussed in the chapter.