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

  1. P A Maroney,
  2. C M Romfo, and
  3. T W Nilsen
  1. Center for RNA Molecular Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.

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.

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  1. RNA 6: 1905-1909

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