Nuclease protection of RNAs containing site-specific labels: A rapid method for mapping RNA-protein interactions

Abstract

This report describes a method that combines nuclease protection and site-specific labeling to determine sites and extents of RNA-protein interactions. The utility of the method is demonstrated by the analysis of the binding of factors to the 3' splice site region of a pre-mRNA labeled at three specific positions. This 'reverse footprinting' technique should be widely applicable to a variety of questions concerning RNA-protein interactions.