Mapping Protein–RNA Interactions by RCAP, RNA-Cross-Linking and Peptide Fingerprinting

  • Robert C. VaughanEmail author
  • C. Cheng Kao
Part of the Methods in Molecular Biology book series (MIMB, volume 1297)


RNA nanotechnology often feature protein RNA complexes. The interaction between proteins and large RNAs are difficult to study using traditional structure-based methods like NMR or X-ray crystallography. RCAP, an approach that uses reversible-cross-linking affinity purification method coupled with mass spectrometry, has been developed to map regions within proteins that contact RNA. This chapter details how RCAP is applied to map protein–RNA contacts within virions.

Key words

Cross-linking immunoprecipitation RNA virion Protein–RNA interaction Mass Spectrometry RCAP Amidination protection 



This work was supported by a grant from the NIH NIAID 1R01AI090280. We thank C.T. Ranjith-Kumar, William Running, James Reilly, and Jonathan Karty for helpful discussions and reagents used to determine the conditions for the protocols in this work.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Molecular and Cellular BiochemistryIndiana UniversityBloomingtonUSA

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