Pa. Maroney et al., Nuclease protection of RNAs containing site-specific labels: A rapid method for mapping RNA-protein interactions, RNA, 6(12), 2000, pp. 1905-1909
This report describes a method that combines nuclease protection and site-s
pecific 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 spec
ific positions. This "reverse footprinting" technique should be widely appl
icable to a variety of questions concerning RNA-protein interactions.