Large libraries reveal diverse solutions to an RNA recognition problem
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.
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.
Published - PNAS-2001-Barrick-12374-8.pdf