Abstract
RNA nanotechnology often involves protein–RNA complexes that require significant understanding of how the proteins and RNAs contact each other. The CLIP-Seq (cross-linking immunoprecipitation, and DNA sequencing) protocol can be used to probe the RNA molecules that interact with proteins. We have optimized the procedures for RNA fragmentation, immunoprecipitation, and library construction in CLIP-Seq to map the interactions between the RNA and the capsid of a simple positive-strand RNA virus. The results show that distinct portions of the viral RNA contact the capsid. The protocol should be applicable to other RNA virions and also RNA–protein nanoparticles.
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Acknowledgement
This work was supported by a grant from the NIH NIAID 1R01AI090280. We thank S. Middleton and R. Qi for helpful discussions and reagents used in this work.
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Fan, B., Ni, P., Kao, C.C. (2015). Mapping RNA Interactions to Proteins in Virions Using CLIP-Seq. 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_15
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DOI: https://doi.org/10.1007/978-1-4939-2562-9_15
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