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RNA Nanotechnology and Therapeutics pp 225–236Cite as

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

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1297))

Abstract

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.

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Acknowledgement

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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Authors and Affiliations

  1. Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne St., 201A Simon Hall, Bloomington, IN, 47405, USA

    Robert C. Vaughan & C. Cheng Kao

Authors
  1. Robert C. Vaughan
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  2. C. Cheng Kao
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Corresponding author

Correspondence to Robert C. Vaughan .

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Editors and Affiliations

  1. Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA

    Peixuan Guo

  2. Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA

    Farzin Haque

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Vaughan, R.C., Kao, C.C. (2015). Mapping Protein–RNA Interactions by RCAP, RNA-Cross-Linking and Peptide Fingerprinting. In: Guo, P., Haque, F. (eds) RNA Nanotechnology and Therapeutics. Methods in Molecular Biology, vol 1297. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2562-9_16

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  • DOI: https://doi.org/10.1007/978-1-4939-2562-9_16

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2561-2

  • Online ISBN: 978-1-4939-2562-9

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