Label-Free Determination of the Kinetic Parameters of Protein-Aptamer Interaction by Surface Plasmon Resonance

Due to their high specificity and affinity to target molecules, aptamers can be used as powerful tools in diagnostics, therapeutics, and environmental or food analytics. For the use in various applications, the detailed characterization of their binding behavior is an important step after selection to determine the interaction strength between the aptamer and its target and to find the best kinetics depending on the field of application. The surface plasmon resonance (SPR) spectroscopy is a powerful technology to investigate important parameters in molecular interaction, for example, kinetics, affinity, and specificity. The most-used system is the Biacore™ SPR system which comprises an optical biosensor for label-free monitoring of binding events in real time based on SPR. This biophysical phenomenon describes the changes in refractive index on a sensor surface which can be used to measure binding events and to determine kinetic constants. In this chapter, a detailed protocol for the determination of kinetic constants for protein-aptamer interaction is provided. An 82-nt long ssDNA aptamer which are targeted against human urokinase is used as a model system for determination of binding and dissociation constants using Biacore™ SPR technology. A detailed note section provides useful tips and pitfalls at the end of this chapter.