title: Selection of RNA-binding peptides in vivo.
abstract: Many priniciples of sequence-specific DNA recognition have been established over the past decade, largely from structural studies of protein-DNA and drug-DNA complexes. On the basis of these principles, it has been possible to design or select variants of known structural motifs, including zinc-fingers and minor groove-binding drugs, that bind desired sequences. Here we describe a strategy, based on transcriptional termination in bacteria, to identify specific RNA-binding peptides using the arginine-rich RNA-binding motif as a framework. Peptides were isolated from two combinatorial libraries that bind tightly and specifically to the Rev response element of HIV. It appears that alpha-helical peptides resembling Rev were selected from one library whereas new peptides that probably do not form helices were selected from the other, suggesting that the arginine-rich motif may be a particularly versatile framework for recognizing RNA structures.
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA.
authors.forename: K
authors.initials: K
authors.lastname: Harada
authors.forename: S S
authors.initials: SS
authors.lastname: Martin
authors.forename: A D
authors.initials: AD
authors.lastname: Frankel
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000378:metabolism; D001483:Base Sequence; D003001:Cloning, Molecular; D015723:Gene Library; D015694:Gene Products, rev / Q000235:genetics / Q000378:metabolism; D015696:Gene Products, tat / Q000235:genetics / Q000378:metabolism; D006678:HIV / Q000378:metabolism; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides; D011485:Protein Binding; D017433:Protein Structure, Secondary; D016601:RNA-Binding Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D054334:Viral Regulatory and Accessory Proteins / Q000378:metabolism; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus
chemical_list: D015694:Gene Products, rev; D015696:Gene Products, tat; C059417:N protein, Bacteriophage lambda; D009838:Oligodeoxyribonucleotides; D016601:RNA-Binding Proteins; D054334:Viral Regulatory and Accessory Proteins; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus; D001120:Arginine