An in vitro-selected RNA receptor for the GAAC loop: Modular receptor for non-GNRA-type tetraloop

Junya Ishikawa, Hiroyuki Furuta, Yoshiya Ikawa

    Research output: Contribution to journalArticlepeer-review

    9 Citations (Scopus)

    Abstract

    Although artificial RNA motifs that can functionally replace the GNRA/receptor interaction, a class of RNA-RNA interacting motifs, were isolated from RNA libraries and used to generate designer RNA structures, receptors for non-GNRA tetraloops have not been found in nature or selected from RNA libraries. In this study, we report successful isolation of a receptor motif interacting with GAAC, a non-GNRA tetraloop, from randomized sequences embedded in a catalytic RNA. Biochemical characterization of the GAAC/receptor interacting motif within three structural contexts showed its binding affinity, selectivity and structural autonomy. The motif has binding affinity comparable with that of a GNRA/receptor, selectivity orthogonal to GNRA/receptors and structural autonomy even in a large RNA context. These features would be advantageous for usage of the motif as a building block for designer RNAs. The isolated motif can also be used as a query sequence to search for unidentified naturally occurring GANC receptor motifs.

    Original languageEnglish
    Pages (from-to)3748-3759
    Number of pages12
    JournalNucleic acids research
    Volume41
    Issue number6
    DOIs
    Publication statusPublished - Apr 2013

    All Science Journal Classification (ASJC) codes

    • Genetics

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