Detection of Nucleic Acid Interactions Using Surface Plasmon Resonance

Several different methods can be used for detection of interactions between RNA and other molecules (e.g., proteins and other nucleic acids). Among these are: (1) enzymatic assays in which there is a measurable change in the property of the substrate such as an increase or decrease in size (mobility in gels or solubility in trichloroacetic acid), (2) gel-shift assays in which the interaction can be detected by altered migration of a complex in gel-electrophoretic analysis, (3) Northwestern assays and Northern analysis in which either proteins or RNA are transferred to a membrane after gel electrophoresis and RNAs are added in solution to interact with the protein or anneal with the RNA on the membrane and others. Each of these techniques has advantages and limitations.