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Large libraries reveal diverse solutions to an RNA recognition problem

Barrick, Jeffrey E. and Takahashi, Terry T. and Ren, Jinsong and Xia, Tianbing and Roberts, Richard W. (2001) Large libraries reveal diverse solutions to an RNA recognition problem. Proceedings of the National Academy of Sciences of the United States of America, 98 (22). pp. 12374-12378. ISSN 0027-8424. PMCID PMC60061. doi:10.1073/pnas.221467798.

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RNA loops that adopt a characteristic GNRA “tetraloop” fold are common in natural RNAs. Here, we have used in vitro selection by means of mRNA-peptide fusions to select peptides that bind an example of this RNA loop motif. Starting with the RNA recognition domain from the λ N protein, we have constructed libraries containing 150, 1,600, and 9 trillion different peptide sequences as mRNA-peptide fusions and isolated those capable of high-affinity RNA binding. These selections have resulted in more than 80 different peptides that bind the same RNA loop. The highest affinity peptides exhibit low nanomolar dissociation constants as well as the ability to discriminate RNA hairpins differing by a single loop nucleotide. Thus, our work demonstrates that numerous, chemically distinct solutions exist for a particular RNA recognition problem.

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URLURL TypeDescription DOIArticle CentralArticle
Roberts, Richard W.0000-0002-8587-5097
Additional Information:© 2001 National Academy of Sciences. Communicated by Donald M. Crothers, Yale University, New Haven, CT, September 4, 2001 (received for review June 15, 2001). We thank Prof. S. L. Mayo, Prof. D. C. Rees, Prof. M. J. Matari'c, R. Austin, S. Li, and B. Ja for comments on the manuscript and T. Snyder for his work defining the round 0 clones. This work was supported by grants from the National Science Foundation (to R.W.R.), National Institutes of Health (to R.W.R.), and Beckman Foundations (to R.W.R.). The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. §1734 solely to indicate this fact.
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Arnold and Mabel Beckman FoundationUNSPECIFIED
Issue or Number:22
PubMed Central ID:PMC60061
Record Number:CaltechAUTHORS:20141121-141034040
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Official Citation:Jeffrey E. Barrick, Terry T. Takahashi, Jinsong Ren, Tianbing Xia, and Richard W. Roberts Large libraries reveal diverse solutions to an RNA recognition problem PNAS 2001 98 (22) 12374-12378; doi:10.1073/pnas.221467798
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:52055
Deposited By: Tony Diaz
Deposited On:21 Nov 2014 22:27
Last Modified:10 Nov 2021 19:20

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