Surface plasmon resonance biosensor analysis of RNA-small molecule interactions

Abstract

Surface plasmon resonance (SPR) biosensors are firmly established for monitoring macromolecular interactions and are becoming a popular technique for characterizing small molecule complexes. SPR biosensors are amenable to the study of kinetics and equilibrium properties of many systems as well as screening of combinatorial libraries, and the potential applications of biosensors are rapidly expanding. Only more recently, however, has the technology advanced to the point that small molecule systems can be studied without the need for a high molecular weight tag. SPR biosensors offer an excellent method for investigating small molecule-macromolecule systems because many small molecules are either not fluorescent or do not yield notable gel band shifts on binding to macromolecules. In addition, such small quantities are required so that precious or sparse samples can be investigated with minimal material requirements. This is in direct contrast to UV or CD spectroscopies, where a 10- to 100-fold increase in sample quantity may be necessary to obtain a satisfactory signal-to-noise ratio. An advantage of SPR is that the method simultaneously can provide kinetic and equilibrium characterization of the interactions of active compounds with macromolecules. When one of the interacting species can be captured on a biosensor surface, the advantages of SPR over conventional interaction analyses can be numerous. SPR monitors molecular interactions in real time and is a significant improvement over optical methods for systems involving strong binding and/or low absorbance or fluorescence.