Thiosulfate-Hydrogen Peroxide Redox Oscillator as pH Driver for Ribozyme Activity in the RNA World. - Abstract. Thiosulfate-Hydrogen Peroxide Redox Oscillator as pH Driver for Ribozyme Activity in the RNA World. Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors. BevilacquaLab sur Twitter : "#ACSBoston Come check out our work on #ribozyme experiments and theory! 8/20. 9:40 am/254A Boston Convention Center. Ribozyme-Spherical Nucleic Acids. National Center for Biotechnology Information. BurkeLab sur Twitter : "Melissa uses ribozymes to tune functional activities of other RNAs: RNA-on-RNA covalent regulation. @MelissaPrasangi. 2N3Q Structure Summary. 2N3R Structure Summary. The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
Artificial Ligase Ribozymes Isolated by a “Design and Selection” Strategy. An origin story: ribozyme catalysis by the ribosome. Twitter. RNA Synthesis by in Vitro Selected Ribozymes for Recreating an RNA World. Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme. Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability. Abstract: The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge.
One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristoleic acid (MA) vesicles at varying concentrations of Mg2+. The ligation rate is significantly lower at low-Mg2+ conditions. 4RGE Structure Summary. 4RGF Structure Summary. Cross-chiral Ribozyme May Hold Clues To Origin Of Life. 4PR6 Structure Summary. 4PRF Structure Summary.
2MTJ Structure Summary. 2MTK Structure Summary. Todd Smith sur Twitter : "From @MoleculeWorld! A group 1 lariat ribozyme (space fill, residue coloring) to accompany my last tweet. Ribozyme Swaps Genes With A Flip Of A Switch. One serious limitation with current gene therapy strategies is a lack of control.
When researchers deliver a gene to replace one linked to disease, there’s no way to turn on the therapeutic gene at the right place and the right time, limiting efficacy and potentially triggering serious side effects. In an effort to take control, researchers developed a catalytic RNA—a ribozyme— that exchanges genes only in the presence of a specific small molecule (ACS Chem. Biol. 2014, DOI: 10.1021/cb500567v). Side effects arise in gene therapy when the therapeutic gene inserts itself into genes not linked to disease, possibly disrupting the function of essential genes or activating a cancer-causing gene. Seong-Wook Lee of Dankook University, in South Korea, and colleagues wanted to gain more control over gene splicing through a ribozyme they could turn off and on. Looking at LncRNAs with the Ribozyme Toolkit: Molecular Cell. To view the full text, please login as a subscribed user or purchase a subscription.
Click here to view the full text on ScienceDirect. A diverse population of large RNA molecules controls every aspect of cellular function, and yet we know very little about their molecular structures. However, robust technologies developed for visualizing ribozymes and riboswitches, together with new approaches for mapping RNA inside cells, provide the foundation for visualizing the structures of long noncoding RNAs, mRNAs, and viral RNAs, thereby facilitating new mechanistic insights. Register an Account If you do not have an account, create one by clicking the button below, and take full advantage of this site's features. Search through over 11 million science, health, medical journal full text articles and books.
Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis. Abstract: The R3C ligase ribozyme is an artificial ligase ribozyme produced by modification of the ribozyme that lacks cytidine.
Here, we attempted to modify the original R3C ribozyme (73 nucleotides) by reducing the number of nucleotides while maintaining the maximum possible catalytic efficiency. By partially deleting both the “grip” (P4 + P5) and “hammer” (P3) stem-loops, we found the critical border to retain activity comparable to that of full-length R3C. The three-way junction structure was necessary to maintain enzymatic function and the stability of the “grip” (P4 + P5) stem had a large influence on the catalytic activity of R3C. The final minimized ribozyme we obtained comprised ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Our findings suggest that the autocatalytic function in ribozymes is indeed possible to obtain using sequence lengths achievable with prebiotic synthesis.
Kurihara, E.; Uchida, S.; Umehara, T.; Tamura, K. A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis. Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis. 4OJI Structure Summary. 4P8Z Structure Summary. 4P95 Structure Summary. 4P9R Structure Summary. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. The wide expansion of hepatitis delta virus-like ribozymes throughout trypanosomatid genomes is linked to the spreading of L1Tc/ingi clade mobile elements.
Research article Francisco José Sánchez-Luque1, Manuel Carlos López1*, Patricia Eugenia Carreira1, Carlos Alonso2 and María Carmen Thomas1* * Corresponding authors: Manuel C López mclopez@ipb.csic.es - María C Thomas mcthomas@ipb.csic.es Author Affiliations 1 Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC, Parque Tecnológico de Ciencias de la Salud, Av. del Conocimiento s/n, 18016 Granada, Spain 2 Centro de Biología Molecular “Severo Ochoa”, CSIC-UAM, Campus Universidad Autónoma de Madrid, C/Nicolás Cabrera n°1, 28049 Madrid, Spain For all author emails, please log on.
RNA Aminoacylation Mediated by Sequential Action of Two Ribozymes and a Nonactivated Amino Acid - Xu - 2014 - ChemBioChem. 2M5U Structure Summary. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing. 2MIS Structure Summary. 2MI0 Structure Summary. Trans-splicing with the group I intron ribozyme from Azoarcus. RNA. Trans-splicing with the group I intron ribozyme from Azoarcus. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP. Open AccessThis article isfreely availablere-usable Article 1 Fondazione "Istituto Pasteur-Fondazione Cenci-Bolognetti" c/o Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, P.le Aldo Moro, 5, Rome 00185, Italy 2 Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy 3 Dipartimento di Scienze Biochimiche, "Sapienza" Università di Roma, P.le Aldo Moro, 5, Rome 00185, Italy 4 Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno 61265, Czech Republic * Author to whom correspondence should be addressed.
Received: 13 September 2013; in revised form: 19 November 2013 / Accepted: 22 November 2013 / Published: 3 December 2013. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP. RNA - The Discovery of Ribozymes (1-2) 4MEG Structure Summary. 4MEH Structure Summary. Group II intron–ribosome association protects intron RNA from degradation. RNA - The Discovery of Ribozymes (1-2) Catalytic activity of hammerhead ribozymes in a clay mineral environment: Implications for the RNA world. Abstract The hypothesized RNA-based world would have required the presence of a protected environment in which RNA, or an RNA-like molecule, could originate and express its biological activity.
Recent studies have indicated that RNA molecules adsorbed/bound on clay minerals are able to persist in the presence of degrading agents, to interact with surrounding molecules, and to transmit the information contained in their nucleotide sequences. In this study, we assessed the ability of RNA molecules with catalytic activity to perform a specific reaction in a mineral environment. For this purpose, we investigated the self-cleavage reaction of the hammerhead ribozyme of the Avocado Sun Blotch Viroid (ASBVd), both in the monomeric and in dimeric forms. The monomeric transcript was tightly bound on the clay mineral montmorillonite to form a stable complex, while the behaviour of the dimeric transcript was studied in the presence of the clay particles in the reaction mixture.
Abbreviations Keywords. An engineered small RNA-mediated genetic switch based on a ribozyme expression platform. + Author Affiliations ↵ *To whom correspondence should be addressed.
Tel: +49 7531 884 575 ; Fax: +49 7531 885 140 ; Email: joerg.hartig@uni-konstanz.de Received November 13, 2012. Revision received March 11, 2013. Accepted March 20, 2013. 2M58 Structure Summary. 3ZP8 Structure Summary. Forskningsdatabasen.dk. Search in more than 500.000 records from all Danish universities and a number of Danish research institutions. more document types Search tips You can make more precise and/or complex search queries by using DDFs prefixes and search operators – get tips on how to make your searches better below.
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Activation of PKR by RNA misfolding: HDV ribozyme dimers activate PKR. + Author Affiliations + Author Notes ↵1 Present address: Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA Abstract Protein Kinase R (PKR), the double-stranded RNA (dsRNA)-activated protein kinase, plays important roles in innate immunity. A small ribozyme with dual-site kinase activity. A strategy for developing a hammerhead ribozyme for selective RNA cleavage depending on substitutional RNA editing. Exploring purine N7 interactions via atomic mutagenesis: The group I ribozyme as a case study.