Native gel electrophoresis to study the binding and release of RNA polymerase by 6S RNA

Abstract

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. © 2012 Springer Science+Business Media, LLC.