Scaffold-independent analysis of RNA-protein interactions: the Nova-1 KH3-RNA complex.

  title={Scaffold-independent analysis of RNA-protein interactions: the Nova-1 KH3-RNA complex.},
  author={Barbara Beuth and M{\^a}ria Flor Garc{\'i}a-Mayoral and Ian A Taylor and Andres Ramos},
  journal={Journal of the American Chemical Society},
  volume={129 33},
We describe a method to analyze the sequence specificity of an RNA-binding domain. The method, which we have named scaffold-independent analysis, reports on the specificity for each nucleotide position within an RNA target, uncoupled from the surrounding structural and sequence context. We expect this information to improve our understanding of protein-RNA interfaces in ssRNA binding domains (e.g., KH or RRM domains) and to be useful to the design of novel protein-RNA recognition surfaces. Our… CONTINUE READING
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