Relevant bibliographies by topics / Riboregulator

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Riboregulator'

Author: Grafiati
Published: 4 June 2021
Last updated: 17 February 2022

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Journal articles on the topic "Riboregulator"

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Rostain, William, Shensi Shen, Teresa Cordero, Guillermo Rodrigo, and Alfonso Jaramillo. "Engineering a Circular Riboregulator in Escherichia coli." BioDesign Research 2020 (September 14, 2020): 1–9. http://dx.doi.org/10.34133/2020/1916789.

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RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli. We showed that the resulting riboregulator can trans-activate gene expression by interacting with a cis-repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled this novel posttranscriptional mechanism. This first reported example of a circular RNA regulating gene expression in E. coli adds to an increasing repertoire of RNA synthetic biology parts, and it highlights that topological molecules can play a role in the case of prokaryotic regulation.
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Nechooshtan, Gal, Maya Elgrably-Weiss, Abigail Sheaffer, Eric Westhof, and Shoshy Altuvia. "A pH-responsive riboregulator." Genes & Development 23, no. 22 (November 15, 2009): 2650–62. http://dx.doi.org/10.1101/gad.552209.

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Narita, Atsushi, Kazumasa Ogawa, Shinsuke Sando, and Yasuhiro Aoyama. "Highly sensitive genotyping using artificial riboregulator system." Nucleic Acids Symposium Series 49, no. 1 (September 1, 2005): 271–72. http://dx.doi.org/10.1093/nass/49.1.271.

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WANG, YANHONG, KELVIN J. A. DAVIES, J. ANDRES MELENDEZ, and DANA R. CRAWFORD. "Characterization of adapt33, a Stress-Inducible Riboregulator." Gene Expression 11, no. 2 (January 1, 2003): 85–94. http://dx.doi.org/10.3727/000000003108748982.

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Krishnamurthy, Malathy, Scott P. Hennelly, Taraka Dale, Shawn R. Starkenburg, Ricardo Martí-Arbona, David T. Fox, Scott N. Twary, Karissa Y. Sanbonmatsu, and Clifford J. Unkefer. "Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression." ACS Synthetic Biology 4, no. 12 (July 27, 2015): 1326–34. http://dx.doi.org/10.1021/acssynbio.5b00041.

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Ueno, Kinuko, Kaori Tsukakoshi, and Kazunori Ikebukuro. "Riboregulator elements as tools to engineer gene expression in cyanobacteria." Applied Microbiology and Biotechnology 102, no. 18 (July 13, 2018): 7717–23. http://dx.doi.org/10.1007/s00253-018-9221-0.

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Turbant, Florian, Pengzhi Wu, Frank Wien, and Véronique Arluison. "The Amyloid Region of Hfq Riboregulator Promotes DsrA:rpoS RNAs Annealing." Biology 10, no. 9 (September 12, 2021): 900. http://dx.doi.org/10.3390/biology10090900.

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Hfq is a bacterial RNA chaperone which promotes the pairing of small noncoding RNAs to target mRNAs, allowing post-transcriptional regulation. This RNA annealing activity has been attributed for years to the N-terminal region of the protein that forms a toroidal structure with a typical Sm-fold. Nevertheless, many Hfqs, including that of Escherichia coli, have a C-terminal region with unclear functions. Here we use a biophysical approach, Synchrotron Radiation Circular Dichroism (SRCD), to probe the interaction of the E. coli Hfq C-terminal amyloid region with RNA and its effect on RNA annealing. This C-terminal region of Hfq, which has been described to be dispensable for sRNA:mRNA annealing, has an unexpected and significant effect on this activity. The functional consequences of this novel property of the amyloid region of Hfq in relation to physiological stress are discussed.
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M. Cech, Grzegorz, and Agnieszka Szalewska-Pałasz. "THE HFQ PROTEIN - A NOVEL VIEW ON THE WELL-KNOWN RIBOREGULATOR." Postępy Mikrobiologii - Advancements of Microbiology 57, no. 1 (2019): 12–21. http://dx.doi.org/10.21307/pm-2018.57.1.012.

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Willkomm, Dagmar K., and Roland K. Hartmann. "6S RNA – an ancient regulator of bacterial RNA polymerase rediscovered." Biological Chemistry 386, no. 12 (December 1, 2005): 1273–77. http://dx.doi.org/10.1515/bc.2005.144.

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AbstractThe bacterial riboregulator 6S RNA was one of the first non-coding RNAs to be discovered in the late 1960s, but its cellular role remained enigmatic until the year 2000. 6S RNA, only recognized to be ubiquitous among bacteria in 2005, binds to RNA polymerase in a σ factor-dependent manner to repress transcription from a subgroup of promoters. The common feature of a double-stranded rod with a central bulge has led to the proposal that 6S RNA may mimic an open promoter complex.
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Janssen, R. A., and J. W. Mier. "Tropomyosin-2 cDNA lacking the 3' untranslated region riboregulator induces growth inhibition of v-Ki-ras-transformed fibroblasts." Molecular Biology of the Cell 8, no. 5 (May 1997): 897–908. http://dx.doi.org/10.1091/mbc.8.5.897.

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The levels of high molecular weight isoforms of tropomyosin (TM) are markedly reduced in ras-transformed cells. Previous studies have demonstrated that the forced expression of tropomyosin-1 (TM-1) induces reversion of the transformed phenotype of ras-transformed fibroblasts. The effects of the related isoform TM-2 on transformation are less clear. To assess the effects of forced expression of the TM-2 protein on ras-induced tumorigenicity, we introduced a TM-2 cDNA lacking the 3' untranslated region riboregulator into ras-transformed NIH 3T3 fibroblasts. TM-2 expression resulted in a flatter cell morphology and restoration of stress fibers. TM-2 expression also significantly reduced growth rates in low serum, soft agar, and nude mice. The reduced growth rates were associated with a prolongation of G0-G1. To identify the mechanism of TM-2-induced growth inhibition, we analyzed the effects of TM-2 reexpression of ERK and c-jun N-terminal kinase (JNK) activities. Levels of ERK phosphorylation and activity in TM-2-transfected tumor cells were comparable to those in mock-transfected tumor cells. JNK activity was only modestly increased in ras-transformed cells relative to untransformed NIH 3T3 cells and only slightly reduced as result of forced TM-2 expression. We conclude that the partially restored expression of the TM-2 protein induces growth inhibition of ras-transformed NIH 3T3 cells without influencing ERK or JNK activities. Furthermore, the 3' untranslated region riboregulator of the alpha-tropomyosin gene is not needed for the inhibition of ras-induced growth.
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Dissertations / Theses on the topic "Riboregulator"

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Deiorio-Haggar, Kaila. "RNA structures regulating ribosomal protein biosynthesis." Thesis, Boston College, 2015. http://hdl.handle.net/2345/bc-ir:104628.

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Thesis advisor: Michelle M. Meyer
Most commonly known for being the blueprint for proteins, RNA also plays vital roles in gene regulation. Non-coding RNAs, functional RNA molecules that are not translated into proteins, are potential regulatory agents in bacteria. Ribosomal autogenous regulatory elements are short transcribed sequences between the promoter and a protein coding region that regulate expression of their associated gene(s), though they are not themselves translated. These sequences form RNA secondary structures that can regulate at either the transcriptional or translational level. These riboregulators have been well characterized in gram-negative bacteria such as Escherichia coli, but in gram-positive bacteria far less is known regarding how r-proteins are regulated. My main goal has been to find riboregulators of r-protein synthesis in Bacilli and determine their consensus structures and phylogenetic distributions. I have utilized the RNA homology search program Infernal, coupled with our high-capacity genomic context visualization tool, to identify homologues of ribosomal-protein autogenous regulatory RNAs found in Bacilli. The alignments produced from this work determine consensus secondary structures and phylogenetic distribution of these regulator RNAs that provide new insight into the structure and function of these RNAs
Thesis (MS) — Boston College, 2015
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Silistre, Hazel. "Riboregulation in Pseudomonas aeruginosa." Thesis, University of Nottingham, 2016. http://eprints.nottingham.ac.uk/32634/.

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The opportunistic human pathogen Pseudomonas aeruginosa controls virulence, production of secondary metabolites, motility, biofilm formation, growth in anaerobic conditions, intracellular and intercellular signalling and the switch from an acute to a chronic mode of infection at the transcriptional and post-transcriptional levels by modulation of the Gac/Rsm system. Cell density-dependent signal accumulation and environmental stimulators such as pH changes and ion limitation activate the GacS/GacA two-component system which in turn triggers transcription of the small regulatory RNAs RsmY and RsmZ. These sRNAs sequester multiple copies of the RNA-binding protein RsmA, antagonising its function. The RsmA/CsrA proteins act as translational repressors by binding to the GGA-motifs in the untranslated region of target mRNAs and blocking ribosome binding. In this study, the biological function of RsmN, an RsmA homologue with a conserved RNA-binding pocket but a distinct protein folding, the predicted autoregulatory mechanism of RsmN, the nature of target transcripts of RsmN, and the cross-regulation between the two Rsm proteins were investigated. The positive control of proteolytic and elastinolytic activities and swarming motility by RsmN has been demonstrated using single and inducible double deletion mutants of rsmN. Furthermore, rsmN deletion increased microcolony formation during biofilm formation. Regulation by RsmN was most apparent in the absence of RsmA, when rsmN expression was induced via a multicopy plasmid and at temperatures lower than 37°C. The double deletion of rsmA and rsmN affected growth, diminished proteolytic and elastinolytic activities, triggered autolysis and led to the increased secretion of the type VI secretion system protein Hcp1. Moreover, the double deletion of rsmA and rsmN altered the colony morphology of P. aeruginosa. Mutagenesis of the functionally critical, conserved RNA-binding residue which is identified as Arg44 in RsmA and Arg62 in RsmN resulted in the loss of RsmN function. In a genome-wide analysis by RNASeq, target transcripts were co-purified with RsmN from 37°C and 34°C cultures of a wild-type strain expressing rsmN in multicopy numbers. RNASeq results indicated that small regulatory RNAs such as CrcZ, RsmY and RgsA are common targets of RsmN and RsmA, whereas PhrS is a target of RsmN only. Other common RsmA and RsmN targets included transcriptional regulators, heat shock proteins, proteases, starvation response proteins, components of the denitrification pathway, outer membrane proteins required for pore formation, type III and type VI secretion system proteins and RsmA. Transcripts of heat shock proteins, the tss operon genes and rsmA were enriched by RsmN at 37°C but not at 34°C whereas the lasB transcript was enriched by RsmN at 34°C but not at 37°C. Based on the list of common targets of RsmA and RsmN and the results obtained from phenotypic assays, induction of the lytic Pf4 prophage, accumulation of alkyl quinolone or c-di-GMP signalling molecules, imbalanced redox state, carbon starvation, increased membrane permeability, and aggregation of misfolded proteins are suggested as possible mechanisms triggering the excessive autolysis of the rsmNind ΔrsmA mutant under uninducing conditions. The data gathered so far suggests that rsmN is differentially expressed, with increased RsmN activity at temperatures below 37°C in comparison with RsmA, and, RsmA and RsmN collectively contribute to the regulation of secondary metabolite production, motility and microcolony formation in P. aeruginosa.
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Taylor, David C. "SELEX targeting mRNAs : the hunt for novel riboregulators /." free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3013032.

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Callura, Jarred Matthew. "Synthetic biology applications of engineered riboregulation." Thesis, Boston University, 2012. https://hdl.handle.net/2144/32011.

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Thesis (Ph.D.)--Boston University
PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
For synthetic biology to make a lasting impact on real-world problems, further increases in the complexity of biomolecular devices are required. Currently, there is a shortage of orthogonal parts that can be assembled to construct highly complex circuits and networks. RNA molecules are a popular source for synthetic biology parts, due to the versatility and predictability of RNA structures. Previously, our lab developed the engineered riboregulator, a RNA-based gene expression system. The advantages of synthetic riboregulation include: physiologically relevant protein production, component modularity, leakage minimization, rapid response time, tunable gene expression, and the ability to independently riboregulate multiple genes simultaneously using orthogonal riboregulator variants. We performed two sets of in vivo experiments that illustrate these unique features and developed two, higher order synthetic devices based on orthogonal riboregulation: the programmable kill switch and the genetic switchboard. The in vivo experiments involved tracking the localization of the TonB protein and manipulating the SOS DNA damage repair network. These studies highlight the ability of our riboregulator to reveal new insights into microbial physiology. Addressing mounting biosecurity concerns, the programmable kill switch employs two riboregulator variants, which regulate two lambda phage proteins, to induce cell lysis rapidly and selectively. Only when we co-expressed the phage proteins did cell suicide occur, and the circuit can link cell death to four different biological signals. To construct a genetic switchboard, we further increased the number of riboregulators in use by designing two new variants. We directly tested our switchboard in a biosensing setup that reports on four environmental signals in single cells using four differentiable reporters. Finally, we utilized the genetic switchboard in a proof-of-concept metabolic engineering application. The metabolism switchboard regulates four metabolic enzymes that control carbon flux through three, E. coli glucose utilization pathways, and we measured its impressive performance across the RNA, protein, and metabolome scales. All together, the applications described here showcase the considerable real-world potential of the engineered riboregulator.
2031-01-02
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Möller, Philip [Verfasser], Franz [Akademischer Betreuer] Narberhaus, and Danja [Akademischer Betreuer] Schünemann. "Riboregulation and RNA-binding proteins in \(\textit Agrobacterium tumefaciens}\) / Philip Möller. Gutachter: Franz Narberhaus ; Danja Schünemann." Bochum : Ruhr-Universität Bochum, 2016. http://d-nb.info/1095884921/34.

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Norouzi, Masoud. "Development of an RNA array to Protein array (RAPA) platform and its application to gene expression analysis of synthetic riboregulators." Thesis, University of Portsmouth, 2018. https://researchportal.port.ac.uk/portal/en/theses/development-of-an-rna-array-to-protein-array-rapa-platform-and-its-application-to-gene-expression-analysis-of-synthetic-riboregulators(5867a39c-55a4-410a-8e5a-53c347b8a81a).html.

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Kouse, Andrew B. "Thermoregulation of Shigella Dysenteriae Factors by RNA Thermometers." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1407793559.

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Bauriedl, Saskia Corinna [Verfasser], Christoph [Gutachter] Schoen, Jörg [Gutachter] Vogel, and Joachim [Gutachter] Morschhäuser. "The influence of riboregulation on fitness and virulence in Neisseria meningitidis / Saskia Corinna Bauriedl ; Gutachter: Christoph Schoen, Jörg Vogel, Joachim Morschhäuser." Würzburg : Universität Würzburg, 2020. http://d-nb.info/1223851230/34.

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Dequivre, Magali. "Implication des ARN non codant dans la virulence du phytopathogène Agrobacterium fabrum C58." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10016/document.

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L'une des caractéristiques majeures des microorganismes, et donc des bactéries, est qu'ils sont en contact direct avec l'environnement et doivent donc percevoir et répondre rapidement à ses variations. Pour cela, plusieurs niveaux de contrôle existent, et récemment le rôle des ARN non codants régulateurs, ou riborégulateurs, a été mis en lumière comme un mécanisme de contrôle peu couteux et rapide pour la cellule. Chez le phytopathogène Agrobacterium fabrum (anciennement appelé Agrobaterium tumefaciens), la virulence est principalement régulée au niveau transcriptionnel par le système à deux composants VirANirG. L'implication des riborégulateurs dans la virulence d'A.fabrum est encore mal connue et ces travaux de thèse ont eu pour objectif de déterminer l'implication de riborégulateurs dans le cycle infectieux de cette bactérie.Pour cela, nous avons identifié l'ensemble des transcrits d 'A. fabrum C58 en combinant l'utilisation de plusieurs méthodes d'analyses globales et nous avons étudié la fonction de différents candidats transcrits à partir du plasmide Ti (plasmide de virulence). Des souches modifiées dans la production des riborégulateurs candidats ont été construites, Jeurs ARNm cibles ont été prédits et validés, et des tests phénotypiques, en particulier des tests de virulence, ont été réalisés. Ainsi, le séquençage des transcrits de petite taille a permis d'identifier plus d'un millier de riborégulateurs potentiels dont plusieurs sont exprimés à partir de régions en relation avec le cycle infectieux. Nous avons validé 4 de ces petits transcrits comme étant des riborégulateurs puisqu'ils sont de petite taille, non traduits en protéine et fortement structurés (RNAI 111, RNA1083, RNA1059 et RNA1051) . Plus particulièrement, nous avons montré que le riborégulateur RNAI 111 était nécessaire pour la virulence d'A.fabrum C58, et que son action semblait se faire au travers du contrôle post-transcriptionnel de gènes impliqués dans les fonctions de virulence et de transfert du plasmide Ti. Un rôle plus modéré du riborégulateur RNA1083 dans le contrôle du cycle infectieux a également été observé, potentiellement au travers de la modulation de la mobilité et du transfert conjugatif du plasmide Ti. D'autre part, nous avons mis en évidence deux autres riborégulateurs, RNA1059 et RNA1051, qui sont impliqués dans le contrôle du maintien du plasmide Ti via une implication dans la réplication du plasmide (RNA 1059) et via une implication dans un nouveau system de toxine-antitoxine présent sur le plasmide Ti (RNA1051). Ainsi à partir d'une analyse globale nous avons mis en évidence le rôle des riboregulateurs dans les systèmes de mise en place de l'infection bactérienne , soit via le contrôle de facteurs de virulence, soit via le contrôle de la persistance du plasmide responsable de la virulence
One of the main characteristics of microorganisms, including bacteria., is their direct interaction with their environment. They thus need to perceive and quickly answer to its variations. Several steps of control exist, and recently the role of regulatory non-coding RNA, or riboregulator, was highlighted as a fast and economic mechanism of regulation. In the phytopathogen Agrobacterium fabrum (previously named Agrobacterium tumefaciens), the virulence is mainly controlled transcriptionally by the two components system VirANirG. The implication of riboregulators in the virulence of this bacterium is still unknown . The objectives of this thesis were to identify A .fabrum riboregulators and to determine their involvement in the infectious cycle of the bacteria. To this end, we identified small transcripts of A . fabrum C58 strain by combining several global analyses, and we studied the function of different candidates transcribed from the Ti plasmid (the virulence plasmid). Strains modified in the production of these candidates were constructed, their mRNA targets were predicted and validated, and phenotypic analyses -especially virulence tests­ were realized.Thereby, small transcript deep-sequencing allowed the identification of a thousand potential riboregulators, some of them being transcribed from regions related to the infectious cycle. We validated 4 of these transcripts as riboregulators according to their small size, their strong secondary structure and their non-translation into protein (RNAIOS I, RNA1059, RNA1083 and RNAl ll l). In particular, we showed that RNA 1111 was necessary for the virulence of A. fabrum C58, and that it seems to act through the posttranscriptional control of genes implicated in virulence functions and in Ti plasmid conjugation. A more moderated role of RNA 1083 was also observed, potentially by the modulation of the bacterial mobility and of the plasmid conjugation. Furthermore, we highlighted two riboregulators, RNA1059 and RNA1051, involved in the control of the Ti plasmid persistence, through their implication in the replication of the plasmid (RNA1059) and in a toxin-antitoxin system present on the Ti plasmid (RNA1051) .Thus, from a global analysis, we brought out the role of riboregulators in the control of several steps of the infectious cycle of A. fabrum C58, through the control of virulence factors, or through the contrai of the persistence of the main actor of the virulence, the Ti plasmid
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"Sensing and Regulation from Nucleic Acid Devices." Doctoral diss., 2019. http://hdl.handle.net/2286/R.I.53637.

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abstract: The highly predictable structural and thermodynamic behavior of deoxynucleic acid (DNA) and ribonucleic acid (RNA) have made them versatile tools for creating artificial nanostructures over broad range. Moreover, DNA and RNA are able to interact with biological ligand as either synthetic aptamers or natural components, conferring direct biological functions to the nucleic acid devices. The applications of nucleic acids greatly relies on the bio-reactivity and specificity when applied to highly complexed biological systems. This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.
Dissertation/Thesis
Doctoral Dissertation Biochemistry 2019
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Book chapters on the topic "Riboregulator"

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Hagihara, Masaki. "Guanine-Tethered Antisense Oligonucleotides as Synthetic Riboregulators." In Methods in Molecular Biology, 197–207. Totowa, NJ: Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-755-6_14.

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Green, Alexander A. "Construction and In Vivo Testing of Prokaryotic Riboregulators." In RNA Nanostructures, 285–302. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7138-1_19.

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Ueno, Kinuko, Kaori Tsukakoshi, and Kazunori Ikebukuro. "Engineering of Riboregulators for Gene Regulation as a Tool for Synthetic Biology." In Advances in Synthetic Biology, 173–86. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-0081-7_10.

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Othman, Munyati, Siuk M. Ng, and Mohd Firdaus-Raih. "Computational Design and Experimental Implementation of Synthetic Riboswitches and Riboregulators." In Encyclopedia of Bioinformatics and Computational Biology, 568–73. Elsevier, 2019. http://dx.doi.org/10.1016/b978-0-12-809633-8.20144-1.

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Conference papers on the topic "Riboregulator"

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Kasl, H., and D. Georgiev. "A dynamic riboregulator design with a programmable all-or-nothing response." In 2015 European Control Conference (ECC). IEEE, 2015. http://dx.doi.org/10.1109/ecc.2015.7330876.

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