Designed RNAs with Two Peptide-Binding Units as Artificial Templates for Native Chemical Ligation of RNA-Binding Peptides

• Published in: Chembiochem : a European journal of chemical biology 2009-11, Vol.10 (17), p.2745-2752
• Main Authors: Kashiwagi, Norimasa, Yamashita, Kohei, Furuta, Hiroyuki, Ikawa, Yoshiya
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animals; Base Sequence; Dimerization; Models, Molecular; molecular evolution; Molecular Sequence Data; Mutation; native chemical ligation; Nucleic Acid Conformation; Peptides - chemistry; Peptides - metabolism; Protein Conformation; RNA; RNA - chemical synthesis; RNA - chemistry; RNA - genetics; RNA structures; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; template catalysis; Templates, Genetic; Tetrahymena - chemistry; Tetrahymena - genetics; Tetrahymena - metabolism
• ISSN: 1439-4227; 1439-7633
• DOI: 10.1002/cbic.200900392

The template effect plays important roles not only in modern synthetic and enzymatic catalysis but also in the ancient "RNA-polypeptide (RNP) world," which has been postulated to be a crucial stage in the origin of life. To mimic primitive template catalysis of peptide ligations by RNAs, we previously reported the design and synthesis of a ternary RNP complex in which the ligation of two peptides was significantly facilitated by a template RNA with two peptide-binding units. However, RNA molecules also promoted the ligation reaction in a nonspecific manner through electrostatic interactions between RNA and basic peptides. In this study, we suppressed this effect by reducing the length of the original template derived from the Tetrahymena intron RNA. This modification, however, decreased the template ability for the specific reaction. As an alternative RNA that was as effective as the original template, we found that a self-dimerizing RNA was a promising template for peptide ligation without a nonspecific effect.