Affinity analysis between trypsin and aptamers using surface plasmon resonance competition experiments in a steady state

A surface plasmon resonance (SPR) competition experiment in a steady state was developed to determine the binding dissociation constants between a protein and its DNA aptamers. The affinities of a large set of trypsin aptamers selected by magnetic beads-systematic evolution of ligands by exponential enrichment (MB-SELEX) and capillary electrophoresis (CE-SELEX) are obtained only on one single chip. A large number of chips and a considerable amount of time are saved compared with a typical SPR experiment. Additionally, this approach does not require prior knowledge of parameters, such as on or off rates, using a nonlinear fitting with a known dissociation constant and the protein concentration as input. Knowledge on the specificity of protein-aptamer interaction is also obtained by the SPR competition experiment.