Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA

RNA–protein interactions are critical in diverse aspects of gene expression and often serve to mediate regulatory events. Many procedures are available to gain information about RNA–protein interactions. They span from initial identification of an interaction, such as through co-immunoprecipitation studies, to highly detailed atomic resolution definition of the interaction gained from crystallographic and NMR studies. One of the most versatile techniques uses native gel electrophoresis to study RNA–protein complexes, which is often called band shift, gel retardation, or electrophoretic mobility shift assays. Gel shift assays have been used to study a plethora of RNA–protein interactions in all organisms, but here we will use the 6S RNA:RNA polymerase interaction from Escherichia coli as an example to direct discussion of questions that can be addressed, including the ability to follow the dynamics of complexes over time.