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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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ribozyme cassette sequence - by Bioz Stars, 2026-07
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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t etrahymena ribozyme sequence  (New England Biolabs)
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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ribozyme-free water  (Millipore)
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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(A) The sequence and predicted secondary structure of the N79 <t>ribozyme</t> cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).
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Image Search Results


(A) The sequence and predicted secondary structure of the N79 ribozyme cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).

Journal: Bio-protocol

Article Title: Ribozyme-Mediated Knockdown of lncRNA Gene Expression in Drosophila

doi: 10.21769/BioProtoc.5477

Figure Lengend Snippet: (A) The sequence and predicted secondary structure of the N79 ribozyme cassette, as predicted by RNAfold [29], with the cleavage site indicated. (B) Model of ribozyme-mediated cleavage in cis, producing two cleavage fragments that may be susceptible to degradation by exonucleases. This figure is modified from Nyberg et al. [23] with permission from Oxford University Press (license 6070880155798).

Article Snippet: In Benchling, insert the ribozyme cassette sequence, which consists of the N79 ribozyme flanked by flexible linker sequences on both sides.

Techniques: Sequencing, Modification

PCR products (826 bp) amplified from the lncRNA CR45715 gene in uninjected (left) and RNP-injected (right) embryos were subjected to T7 endonuclease I (T7EI) digestion. T7EI digestion of this PCR amplicon was predicted to produce cleavage products of 596 and 230 bp upon successful cleavage and NHEJ by the sgRNA/Cas9 RNP. The 596-bp cleavage product (marked by an arrow) is clearly visible in two of three RNP-injected flies, though the 230-bp product is too faint to visualize. Bands at ~500 and ~300 bp are produced in all embryos, including uninjected, after T7EI digestion and are not indicative of successful targeting by sgRNA/Cas9 RNP. This sgRNA was subsequently used to successfully insert the ribozyme cassette in the CR45715 locus [23]. The figure is reproduced from Nyberg et al. [26] with permission from Springer Nature (license 6070871136981).

Journal: Bio-protocol

Article Title: Ribozyme-Mediated Knockdown of lncRNA Gene Expression in Drosophila

doi: 10.21769/BioProtoc.5477

Figure Lengend Snippet: PCR products (826 bp) amplified from the lncRNA CR45715 gene in uninjected (left) and RNP-injected (right) embryos were subjected to T7 endonuclease I (T7EI) digestion. T7EI digestion of this PCR amplicon was predicted to produce cleavage products of 596 and 230 bp upon successful cleavage and NHEJ by the sgRNA/Cas9 RNP. The 596-bp cleavage product (marked by an arrow) is clearly visible in two of three RNP-injected flies, though the 230-bp product is too faint to visualize. Bands at ~500 and ~300 bp are produced in all embryos, including uninjected, after T7EI digestion and are not indicative of successful targeting by sgRNA/Cas9 RNP. This sgRNA was subsequently used to successfully insert the ribozyme cassette in the CR45715 locus [23]. The figure is reproduced from Nyberg et al. [26] with permission from Springer Nature (license 6070871136981).

Article Snippet: In Benchling, insert the ribozyme cassette sequence, which consists of the N79 ribozyme flanked by flexible linker sequences on both sides.

Techniques: Amplification, Injection, Produced

Workflow for the integration of the ribozyme cassette into the Drosophila genome via homology-directed repair (HDR) and validation of lncRNA knockdown using RT-qPCR and RNA smFISH

Journal: Bio-protocol

Article Title: Ribozyme-Mediated Knockdown of lncRNA Gene Expression in Drosophila

doi: 10.21769/BioProtoc.5477

Figure Lengend Snippet: Workflow for the integration of the ribozyme cassette into the Drosophila genome via homology-directed repair (HDR) and validation of lncRNA knockdown using RT-qPCR and RNA smFISH

Article Snippet: In Benchling, insert the ribozyme cassette sequence, which consists of the N79 ribozyme flanked by flexible linker sequences on both sides.

Techniques: Biomarker Discovery, Knockdown, Quantitative RT-PCR

Important design considerations are depicted at and around the sgRNA target site. The double-strand break (DSB) occurs 3 bp upstream of the NGG PAM site, which is adjacent to the sgRNA target site but not included in the sgRNA itself. The scarless DsRed cassette can be inserted at a nearby TTAA site, ideally within 30 bp of the DSB. The ribozyme cassette itself is inserted between the NGG PAM site and the sgRNA target site within the donor repair plasmid, thus preventing the sgRNA/Cas9 RNP from targeting and cleaving the donor plasmid during injections.

Journal: Bio-protocol

Article Title: Ribozyme-Mediated Knockdown of lncRNA Gene Expression in Drosophila

doi: 10.21769/BioProtoc.5477

Figure Lengend Snippet: Important design considerations are depicted at and around the sgRNA target site. The double-strand break (DSB) occurs 3 bp upstream of the NGG PAM site, which is adjacent to the sgRNA target site but not included in the sgRNA itself. The scarless DsRed cassette can be inserted at a nearby TTAA site, ideally within 30 bp of the DSB. The ribozyme cassette itself is inserted between the NGG PAM site and the sgRNA target site within the donor repair plasmid, thus preventing the sgRNA/Cas9 RNP from targeting and cleaving the donor plasmid during injections.

Article Snippet: In Benchling, insert the ribozyme cassette sequence, which consists of the N79 ribozyme flanked by flexible linker sequences on both sides.

Techniques: Plasmid Preparation