RNA enzymes as tools for gene ablation. by James, W, al-Shamkhani, A

“…Although a number of reports have described ribozymes that are effective in inhibiting gene expression, few studies have attempted, systematically, to analyze the features of ribozymes that affect their potency within cells. …”

Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding by Katharina Semrad

“…RNA chaperone activity is studied in vitro and in vivo using oligonucleotide- or ribozyme-based assays. Due to their functional as well as structural diversity, a common chaperoning mechanism or universal motif has not yet been identified. …”
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New reporters of protein trafficking and protein-protein interactions in live cells by Fernández Suárez, Marta

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A novel method to rescue and culture duck Astrovirus type 1 in vitro by Ruihua Zhang, Jingjing Lan, Haie Li, Junhao Chen, Yupeng Yang, Shaoli Lin, Zhijing Xie, Shijin Jiang

“…Methods In this study, a DNA-launched infectious clone of DAstV-1 was constructed from a cDNA plasmid, which contains a viral cDNA sequence flanked by hammerhead ribozyme (HamRz) and a hepatitis delta virus ribozyme (HdvRz) sequence at both terminals of the viral genome. …”
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Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis by Chen Xiaowei S, Penny David, Collins Lesley J

“…</p> <p>Results</p> <p>We have identified the previously 'missing' <it>Giardia </it>RNase MRP RNA, which is a key ribozyme involved in pre-rRNA processing. We have also uncovered 18 new H/ACA box snoRNAs, expanding our knowledge of the H/ACA family of snoRNAs.…”
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The Place of RNA in the Origin and Early Evolution of the Genetic Machinery by Günter Wächtershäuser

“…The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. …”
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Three Biopolymers and Origin of Life Scenarios by Ilana Agmon

“…It points to the precedence of an RNA–protein system, whose model of emergence suggests specific processes whereby a coded proto-ribosome ribozyme, specifically aminoacylated proto-tRNAs and a proto-polymerase enzyme, could have autonomously emerged, cross-catalyzing the formation of each other. …”
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Sequence specific detection of bacterial 23S ribosomal RNA by TLR13 by Xiao-Dong Li, Zhijian J Chen

“…A sequence containing 13 nucleotides near the active site of 23S rRNA ribozyme, which catalyzes peptide bond synthesis, was both necessary and sufficient to trigger TLR13-dependent interleukin-1β production. …”
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Modulating myoblast differentiation with RNA-based controllers by Peter B. Dykstra, Thomas A. Rando, Christina D. Smolke

“…Here, we describe the application of a theophylline-responsive RNA device in a muscle progenitor cell system to control myogenic differentiation. Ribozyme-based RNA switches responsive to theophylline control fluorescent reporter expression in C2C12 myoblasts in a ligand dependent manner. …”
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A rapid and efficient reverse genetics method for generating RNA viruses by Ms Kavitha Sethumadhavan, Ms JyothiLakshmi Sajimon, Dr Pratyajit Mohapatra, Dr Victor Stalin Raj

“…This involved amplifying the antigenome as five overlapping fragments, excluding the G protein genes, and integrating regulatory elements (T7 promoter, ribozyme, and T7 terminator) into a plasmid vector (pLinker). …”
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Detection of high levels of recombination generated during PCR amplification of RNA templates by Wayne Yu, Karl J. Rusterholtz, Amber T. Krummel, Niles Lehman

“…Three different RNA-encoding DNA templates were assayed: (i)one for a group I ribozyme, (ii)one for a 16S ribosomal RNA (rRNA), and (iii)one for a messenger RNA (mRNA). …”
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The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life by Lei Lei, Zachary Frome Burton

“…From analysis of tRNA evolution, ribozyme-mediated RNA ligation was a primary driving force in the evolution of complexity during the pre-life-to-life transition. …”
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The brown algae Pl.LSU/2 group II intron-encoded protein has functional reverse transcriptase and maturase activities. by Madeleine Zerbato, Nathalie Holic, Sophie Moniot-Frin, Dina Ingrao, Anne Galy, Javier Perea

“…The brown algae Pylaiella littoralis Pl.LSU/2 group II intron is uniquely capable of in vitro ribozyme activity at physiological level of magnesium but this intron remains poorly characterized. …”
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PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies by Guoliang Yuan, Stanton Martin, Md Mahmudul Hassan, Gerald A. Tuskan, Xiaohan Yang

“…Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.…”
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Targeted mRNA demethylation in Arabidopsis using plant m6A editor by Ruiqiu Fang, Xiaolong Chen, Jie Shen, Bin Wang

“…In addition, we discovered that a double ribozyme system can significantly improve the efficiency of RNA editing. …”
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Mimicking the in vivo Environment – The Effect of Crowding on RNA and Biomacromolecular Folding and Activity by Erica Fiorini, Richard Börner, Roland K. O. Sigel

“…Herein, we refer to a collection of examples for proteins and nucleic acids and their interactions in crowding environments and present in detail the effect of cosolutes on RNA folding and activity using a group II intron ribozyme as an example. …”
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Modulating myoblast differentiation with RNA-based controllers. by Peter B Dykstra, Thomas A Rando, Christina D Smolke

“…Here, we describe the application of a theophylline-responsive RNA device in a muscle progenitor cell system to control myogenic differentiation. Ribozyme-based RNA switches responsive to theophylline control fluorescent reporter expression in C2C12 myoblasts in a ligand dependent manner. …”
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Recapitulation of Werner syndrome sensitivity to camptothecin by limited knockdown of the WRN helicase/exonuclease. by Bird, J, Jennert-Burston, K, Bachler, M, Mason, P, Lowe, J, Heo, S, Campisi, J, Faragher, R, Cox, L

“…We show that targeting WRN mRNA for degradation by either RNAi or hammerhead ribozyme catalysis renders human fibroblasts as sensitive to CPT as fibroblasts derived from WS patients, and furthermore, we find altered cell cycle transit and nucleolar destabilisation in these cells following CPT treatment. …”

Deadenylation is a widespread effect of miRNA regulation. by Eulalio, A, Huntzinger, E, Nishihara, T, Rehwinkel, J, Fauser, M, Izaurralde, E

“…However, neither a poly(A) tail nor mRNA circularization are required for silencing, because mRNAs whose 3' ends are generated by a self-cleaving ribozyme are also silenced in vivo. We show further that miRNAs trigger mRNA degradation, even when binding by 40S ribosomal subunits is inhibited in cis. …”

Mapping the kinetic barriers of a Large RNA molecule's folding landscape. by Jörg C Schlatterer, Joshua S Martin, Alain Laederach, Michael Brenowitz

“…We applied Eyring's theory to time-resolved hydroxyl radical (•OH) footprinting kinetics progress curves collected at eight temperature from 21.5 °C to 51 °C to characterize the thermodynamic nature of folding intermediate formation for the Mg(2+)-mediated folding of the Tetrahymena thermophila group I ribozyme. A common kinetic model configuration describes this RNA folding reaction over the entire temperature range studied consisting of primary (fast) transitions to misfolded intermediates followed by much slower secondary transitions, consistent with previous studies. …”
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