Sensing complex regulatory networks by conformationally controlled hairpin ribozymes

Hani Najafi, Günter Mayer, Michael Famulok

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

The hairpin ribozyme catalyses RNA cleavage by a mechanism utilizing its conformational flexibility during the docking of two independently folded internal loop domains A and B. Based on this mechanism, we designed hairpin ribozyme variants that can be induced or repressed by external effector oligonucleotides influencing the docking process. We incorporated a third domain C to assimilate alternate stable RNA motifs such as a pseudo-half-knot or an internal stem-loop structure. Small sequence changes in domain C allowed targeted switching of ribozyme activity: the same effector oligonucleotide can either serve as an inducer or repressor. The ribozymes were applied to trp leader mRNA, the RNA sequence tightly bound by L-tryptophan-activated trp-RNA-binding attenuation protein (TRAP). When domain C is complementary to this mRNA, ribozyme activity can be altered by annealing trp leader mRNA, then specifically reverted by its TRAP/tryptophan-mediated sequestration. This approach allows to precisely sense the activity status of a protein controlled by its metabolite molecule.

Original languageEnglish
Pages (from-to)3212-3219
Number of pages8
JournalNucleic Acids Research
Volume32
Issue number10
DOIs
Publication statusPublished - 2004
Externally publishedYes

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Catalytic RNA
RNA-Binding Proteins
Oligonucleotides
Tryptophan
RNA Cleavage
Messenger RNA
Nucleotide Motifs
5' Untranslated Regions
hairpin ribozyme
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. / Najafi, Hani; Mayer, Günter; Famulok, Michael.

In: Nucleic Acids Research, Vol. 32, No. 10, 2004, p. 3212-3219.

Research output: Contribution to journalArticle

Najafi, Hani ; Mayer, Günter ; Famulok, Michael. / Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. In: Nucleic Acids Research. 2004 ; Vol. 32, No. 10. pp. 3212-3219.
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