Evolutionary optimization of a modular ligase ribozyme: A small catalytic unit and a hairpin motif masking an element that could form an inactive structure

Yuki Fujita, Hiroyuki Furuta, Yoshiya Ikawa

    Research output: Contribution to journalArticlepeer-review

    5 Citations (Scopus)

    Abstract

    The YFL ribozyme is an artificial ligase ribozyme isolated by a 'design and selection' strategy, in which a modular catalytic unit was generated on a rationally designed modular scaffold RNA. This ligase ribozyme has a versatile catalytic unit that accepts not only β-nicotinamide mononucleotide (β-NMN) but also inorganic pyrophosphate as leaving groups for template-dependent RNA ligation. Although this property is interesting from an evolutionary viewpoint regarding primitive RNA ligation/polymerization systems in the RNA world, structural analysis of the YFL ribozyme has not been continued due to apparent structural nonuniformity of its folded state. To elucidate the active structure of the YFL ribozyme, we performed in vitro evolution experiments to improve its folding ability. Biochemical and phylogenetic analyses of evolved variants indicated that the catalytic unit of the YFL ribozyme is compact and the 3′ singlestranded region of the parent YFL-1 ribozyme contributes to mask an element that could form an inactive structure.

    Original languageEnglish
    Article numbergkq018
    Pages (from-to)3328-3339
    Number of pages12
    JournalNucleic acids research
    Volume38
    Issue number10
    DOIs
    Publication statusPublished - Jan 27 2010

    All Science Journal Classification (ASJC) codes

    • Genetics

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