Surface Plasmon Resonance Investigation of RNA Aptamer–RNA Ligand Interactions

Abstract

Instruments based on the surface plasmon resonance (SPR) principle allow label-free detection of interactions between targets immobilized at a solid–liquid interface and partners in solution. This method is well suited to determine the kinetic parameters, the equilibrium constant and the stoichiometry of a reaction. Aptamers are ligands identified from random libraries of RNA, DNA or chemically modified oligonucleotides by in vitro selection (SELEX). Aptamers can be raised against a great variety of targets (small molecules, proteins, nucleic acids, cells, viruses, bacteria). SPR is routinely used in our laboratory for the analysis of RNA aptamer–RNA target complexes. To illustrate SPR investigation of such complexes, we describe here methods that were successfully used to monitor the interaction between the trans-activating responsive element of HIV-1 and an RNA aptamer.