Experimental models of protein-RNA interaction: Isolation and analyses of tRNA(Phe) and U1 snRNA-binding peptides from bacteriophage display libraries

Peptides that bind either U1 small nuclear RNA (U1 snRNA) or the anticodon stem and loop of yeast tRNA(Phe) (tRNAP(AC)(Phe)) were selected from a rand om-sequence, 15-amino acid bacteriophage display library. An experimental s ystem, including an affinity selection method, was designed to identify pri mary RNA-binding peptide sequences without bias to known amino acid sequenc es and without incorporating nonspecific binding of the anionic RNA backbon e. Nitrocellulose binding assays were used to evaluate the binding of RNA b y peptide-displaying bacteriophage. Amino acid sequences of RNA-binding bac teriophage were determined from the foreign insert DNA sequences, and pepti des corresponding to the RNA-binding bacteriophage inserts were chemically synthesized. Peptide affinities for the RNAs (K-d approximate to 0.1-5.0 mu M) were analyzed successfully using fluorescence and circular dichroism sp ectroscopies. These methodologies demonstrate the feasibility of rapidly id entifying, isolating, and initiating the analyses of small peptides that bi nd to RNAs in an effort to define better the chemistry, structure, and func tion of protein-RNA complexes.