Journal articles: 'RNA synthetic biology'

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Isaacs, Farren J., Daniel J. Dwyer, and James J. Collins. "RNA synthetic biology." Nature Biotechnology 24, no. 5 (May 2006): 545–54. http://dx.doi.org/10.1038/nbt1208.

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Schmidt, Calvin M., and Christina D. Smolke. "RNA Switches for Synthetic Biology." Cold Spring Harbor Perspectives in Biology 11, no. 1 (January 2019): a032532. http://dx.doi.org/10.1101/cshperspect.a032532.

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Saito, Hirohide, and Tan Inoue. "Synthetic biology with RNA motifs." International Journal of Biochemistry & Cell Biology 41, no. 2 (February 2009): 398–404. http://dx.doi.org/10.1016/j.biocel.2008.08.017.

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Kim, Jongmin, and Elisa Franco. "RNA nanotechnology in synthetic biology." Current Opinion in Biotechnology 63 (June 2020): 135–41. http://dx.doi.org/10.1016/j.copbio.2019.12.016.

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O’Donoghue and Heinemann. "Synthetic DNA and RNA Programming." Genes 10, no. 7 (July 11, 2019): 523. http://dx.doi.org/10.3390/genes10070523.

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Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering as well as omics technologies. Together these technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease. This Special Issue on “Synthetic RNA and DNA Programming” features original research articles and reviews, highlighting novel aspects of basic molecular biology and the molecular mechanisms of disease that were uncovered by the application and development of novel synthetic biology-driven approaches.

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Green, Alexander A. "Synthetic bionanotechnology: synthetic biology finds a toehold in nanotechnology." Emerging Topics in Life Sciences 3, no. 5 (October 23, 2019): 507–16. http://dx.doi.org/10.1042/etls20190100.

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Enabled by its central role in the molecular networks that govern cell function, RNA has been widely used for constructing components used in biological circuits for synthetic biology. Nucleic acid nanotechnology, which exploits predictable nucleic acid interactions to implement programmable molecular systems, has seen remarkable advances in in vitro nanoscale self-assembly and molecular computation, enabling the production of complex nanostructures and DNA-based neural networks. Living cells genetically engineered to execute nucleic acid nanotechnology programs thus have outstanding potential to significantly extend the current limits of synthetic biology. This perspective discusses the recent developments and future challenges in the field of synthetic bionanotechnology. Thus far, researchers in this emerging area have implemented dozens of programmable RNA nanodevices that provide precise control over gene expression at the transcriptional and translational levels and through CRISPR/Cas effectors. Moreover, they have employed synthetic self-assembling RNA networks in engineered bacteria to carry out computations featuring up to a dozen inputs and to substantially enhance the rate of chemical synthesis. Continued advancement of the field will benefit from improved in vivo strategies for streamlining nucleic acid network synthesis and new approaches for enhancing network function. As the field matures and the complexity gap between in vitro and in vivo systems narrows, synthetic bionanotechnology promises to have diverse potential applications ranging from intracellular circuits that detect and treat disease to synthetic enzymatic pathways that efficiently produce novel drug molecules.

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Soll, Dieter. "A tRNA-guided research journey from synthetic chemistry to synthetic biology." RNA 21, no. 4 (March 16, 2015): 742–44. http://dx.doi.org/10.1261/rna.050625.115.

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Benenson, Yaakov. "Synthetic biology with RNA: progress report." Current Opinion in Chemical Biology 16, no. 3-4 (August 2012): 278–84. http://dx.doi.org/10.1016/j.cbpa.2012.05.192.

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Davidson, Eric A., and Andrew D. Ellington. "Synthetic RNA circuits." Nature Chemical Biology 3, no. 1 (December 15, 2006): 23–28. http://dx.doi.org/10.1038/nchembio846.

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Apura, Patrícia, Susana Domingues, Sandra C. Viegas, and Cecília M. Arraiano. "Reprogramming bacteria with RNA regulators." Biochemical Society Transactions 47, no. 5 (October 23, 2019): 1279–89. http://dx.doi.org/10.1042/bst20190173.

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Abstract The revolution of genomics and growth of systems biology urged the creation of synthetic biology, an engineering discipline aiming at recreating and reprogramming cellular functions for industrial needs. There has been a huge effort in synthetic biology to develop versatile and programmable genetic regulators that would enable the precise control of gene expression. Synthetic RNA components have emerged as a solution, offering a diverse range of programmable functions, including signal sensing, gene regulation and the modulation of molecular interactions. Owing to their compactness, structure and way of action, several types of RNA devices that act on DNA, RNA and protein have been characterized and applied in synthetic biology. RNA-based approaches are more ‘economical' for the cell, since they are generally not translated. These RNA-based strategies act on a much shorter time scale than transcription-based ones and can be more efficient than protein-based mechanisms. In this review, we explore these RNA components as building blocks in the RNA synthetic biology field, first by explaining their natural mode of action and secondly discussing how these RNA components have been exploited to rewire bacterial regulatory circuitry.

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Ge, Huanhuan, and Mario Andrea Marchisio. "Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology." Life 11, no. 3 (March 17, 2021): 248. http://dx.doi.org/10.3390/life11030248.

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Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.

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Park, Soyeon V., Jae-Seong Yang, Hyesung Jo, Byunghwa Kang, Seung Soo Oh, and Gyoo Yeol Jung. "Catalytic RNA, ribozyme, and its applications in synthetic biology." Biotechnology Advances 37, no. 8 (December 2019): 107452. http://dx.doi.org/10.1016/j.biotechadv.2019.107452.

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Shis, David L., and Matthew R. Bennett. "Synthetic biology: the many facets of T7 RNA polymerase." Molecular Systems Biology 10, no. 7 (July 2014): 745. http://dx.doi.org/10.15252/msb.20145492.

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Ishikawa, Junya, Hiroyuki Furuta, and Yoshiya Ikawa. "RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology." Wiley Interdisciplinary Reviews: RNA 4, no. 6 (July 8, 2013): 651–64. http://dx.doi.org/10.1002/wrna.1185.

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d'Aquino, Anne E., Do Soon Kim, and Michael C. Jewett. "Engineered Ribosomes for Basic Science and Synthetic Biology." Annual Review of Chemical and Biomolecular Engineering 9, no. 1 (June 7, 2018): 311–40. http://dx.doi.org/10.1146/annurev-chembioeng-060817-084129.

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The ribosome is the cell's factory for protein synthesis. With protein synthesis rates of up to 20 amino acids per second and at an accuracy of 99.99%, the extraordinary catalytic capacity of the bacterial translation machinery has attracted extensive efforts to engineer, reconstruct, and repurpose it for biochemical studies and novel functions. Despite these efforts, the potential for harnessing the translation apparatus to manufacture bio-based products beyond natural limits remains underexploited, and fundamental constraints on the chemistry that the ribosome's RNA-based active site can carry out are unknown. This review aims to cover the past and present advances in ribosome design and engineering to understand the fundamental biology of the ribosome to facilitate the construction of synthetic manufacturing machines. The prospects for the development of engineered, or designer, ribosomes for novel polymer synthesis are reviewed, future challenges are considered, and promising advances in a variety of applications are discussed.

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Duranti, Tiziana, Anna La Teana, Tiziana Cacciamani, and Pietro Volpe. "The Prokaryotic Origin of the Pathways for Synthesis and Post-Synthetic Modification of Deoxyribonucleic Acid." RNA Biology 3, no. 1 (January 2006): 49–53. http://dx.doi.org/10.4161/rna.3.1.2794.

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Zhang, Wenhui, and Qiong Wu. "Applications of phage-derived RNA-based technologies in synthetic biology." Synthetic and Systems Biotechnology 5, no. 4 (December 2020): 343–60. http://dx.doi.org/10.1016/j.synbio.2020.09.003.

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Saito, Hirohide, and Tan Inoue. "RNA and RNP as new molecular parts in synthetic biology." Journal of Biotechnology 132, no. 1 (October 2007): 1–7. http://dx.doi.org/10.1016/j.jbiotec.2007.07.952.

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Wieland, Markus, and Martin Fussenegger. "Ligand-dependent regulatory RNA parts for Synthetic Biology in eukaryotes." Current Opinion in Biotechnology 21, no. 6 (December 2010): 760–65. http://dx.doi.org/10.1016/j.copbio.2010.06.010.

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Dabkowska, Aleksandra P., Agnes Michanek, Luc Jaeger, Michael Rabe, Arkadiusz Chworos, Fredrik Höök, Tommy Nylander, and Emma Sparr. "Assembly of RNA nanostructures on supported lipid bilayers." Nanoscale 7, no. 2 (2015): 583–96. http://dx.doi.org/10.1039/c4nr05968a.

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McDonald, Sarah M. "RNA synthetic mechanisms employed by diverse families of RNA viruses." Wiley Interdisciplinary Reviews: RNA 4, no. 4 (April 18, 2013): 351–67. http://dx.doi.org/10.1002/wrna.1164.

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HANSON, S. "Molecular analysis of a synthetic tetracycline-binding riboswitch." RNA 11, no. 4 (April 1, 2005): 503–11. http://dx.doi.org/10.1261/rna.7251305.

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Hong, Seongho, Dohyun Jeong, Jordan Ryan, Mathias Foo, Xun Tang, and Jongmin Kim. "Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits." Biomolecules 11, no. 8 (August 10, 2021): 1182. http://dx.doi.org/10.3390/biom11081182.

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RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.

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GARCIA-MARTIN, JUAN ANTONIO, PETER CLOTE, and IVAN DOTU. "RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN." Journal of Bioinformatics and Computational Biology 11, no. 02 (April 2013): 1350001. http://dx.doi.org/10.1142/s0219720013500017.

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Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups — for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design — we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver http://bioinformatics.bc.edu/clotelab/RNAiFold ; additionally, the source code can be downloaded from that site.

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Chu, Yongjun, Shinnichi Yokota, Jing Liu, Audrius Kilikevicius, Krystal C. Johnson, and David R. Corey. "Argonaute binding within human nuclear RNA and its impact on alternative splicing." RNA 27, no. 9 (June 9, 2021): 991–1003. http://dx.doi.org/10.1261/rna.078707.121.

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Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNA-seq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between the cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and recapitulated by synthetic miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be natural regulatory mechanisms, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.

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Kremser, J., E. Strebitzer, R. Plangger, M. A. Juen, F. Nußbaumer, H. Glasner, K. Breuker, and C. Kreutz. "Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA." Chemical Communications 53, no. 96 (2017): 12938–41. http://dx.doi.org/10.1039/c7cc06747j.

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Chakraborty, Saikat, Shabana Mehtab, and Yamuna Krishnan. "The Predictive Power of Synthetic Nucleic Acid Technologies in RNA Biology." Accounts of Chemical Research 47, no. 6 (April 8, 2014): 1710–19. http://dx.doi.org/10.1021/ar400323d.

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Lu, Yanyan, Feng-Xia Liang, and Xiaozhong Wang. "A Synthetic Biology Approach Identifies the Mammalian UPR RNA Ligase RtcB." Molecular Cell 55, no. 5 (September 2014): 758–70. http://dx.doi.org/10.1016/j.molcel.2014.06.032.

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Pothoulakis, Georgios, Francesca Ceroni, Benjamin Reeve, and Tom Ellis. "The Spinach RNA Aptamer as a Characterization Tool for Synthetic Biology." ACS Synthetic Biology 3, no. 3 (September 13, 2013): 182–87. http://dx.doi.org/10.1021/sb400089c.

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Han, Dongran, Xiaodong Qi, Cameron Myhrvold, Bei Wang, Mingjie Dai, Shuoxing Jiang, Maxwell Bates, et al. "Single-stranded DNA and RNA origami." Science 358, no. 6369 (December 14, 2017): eaao2648. http://dx.doi.org/10.1126/science.aao2648.

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Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology.

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Anderson, Alex J., Heidi R. Culver, Tania R. Prieto, Payton J. Martinez, Jasmine Sinha, Stephanie J. Bryant, and Christopher N. Bowman. "Messenger RNA enrichment using synthetic oligo(T) click nucleic acids." Chemical Communications 56, no. 90 (2020): 13987–90. http://dx.doi.org/10.1039/d0cc05815g.

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Messenger RNA enrichment is a key step in many molecular biology techniques. Herein, novel poly(T) oligonucleotides, synthesized via cost-effective thiol–ene polymerization, enrich mRNA in yields that rival commercially available techniques

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Jaeger, Luc, and Erin R. Calkins. "Downward causation by information control in micro-organisms." Interface Focus 2, no. 1 (September 29, 2011): 26–41. http://dx.doi.org/10.1098/rsfs.2011.0045.

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The concepts of functional equivalence classes and information control in living systems are useful to characterize downward (or top-down) causation by feedback information control in synthetic biology. Herein, we re-analyse published experiments of microbiology and synthetic biology that demonstrate the existence of several classes of functional equivalence in microbial organisms. Classes of functional equivalence from the bacterial operating system, which processes and controls the information encoded in the genome, can readily be interpreted as strong evidence, if not demonstration, of top-down causation (TDC) by information control. The proposed biological framework reveals how this type of causality is put in action in the cellular operating system. Considerations on TDC by information control and adaptive selection can be useful for synthetic biology by delineating the irreducible set of properties that characterizes living systems. Through a ‘retro-synthetic’ biology approach, these considerations could contribute to identifying the constraints behind the emergence of molecular complexity during the evolution of an ancient RNA/peptide world into a modern DNA/RNA/protein world. In conclusion, we propose TDCs by information control and adaptive selection as the two types of downward causality absolutely necessary for life.

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Grinnell, B. W., and R. R. Wagner. "Inhibition of DNA-dependent transcription by the leader RNA of vesicular stomatitis virus: role of specific nucleotide sequences and cell protein binding." Molecular and Cellular Biology 5, no. 10 (October 1985): 2502–13. http://dx.doi.org/10.1128/mcb.5.10.2502-2513.1985.

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The leader RNA transcript of vesicular stomatitis virus inhibits transcription of the adenovirus major late promoter and virus-associated genes in a soluble HeLa cell transcription system. We examined the specific nucleotide sequence involved and the potential role of leader-protein interactions in this inhibition of RNA polymerase II- and III-directed transcription. Using synthetic oligodeoxynucleotides homologous to regions of the leader RNA molecule, we extend our previous results (B.W. Grinnell and R.R. Wagner, Cell 36:533-543, 1984) that suggest a role for the AU-rich region of the leader RNA or the homologous AT region of a cloned cDNA leader in the inhibition of DNA-dependent transcription. Our results indicate that a short nucleotide sequence (AUUAUUA) or its deoxynucleotide homolog (ATTATTA) appears to be the minimal requirement for the leader RNA to inhibit transcription by both RNA polymerases, but sequences flanking both sides of this region increase the inhibitory activity. Nucleotide changes in the homologous AT-rich region drastically decrease the transcriptional inhibitory activity. Leader RNAs from wild-type virus, but not from a 5'-defective interfering particle, form a ribonuclease-resistant, protease-sensitive ribonucleoprotein complex in the soluble HeLa cell extract. Several lines of evidence suggest that the leader RNA specifically interacts with a 65,000-dalton (65K) cellular protein. In a fractionated cell extract, only those fractions containing this 65K protein could reverse the inhibition of DNA-dependent RNA synthesis by the plus-strand vesicular stomatitis virus leader RNA or by homologous DNA. In studies with synthetic oligodeoxynucleotides homologous to leader RNA sequences, only those oligonucleotides containing the inhibitory sequence were able to bind to a gradient fraction containing the 65K protein.

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Topp, S., and J. P. Gallivan. "Riboswitches in unexpected places--A synthetic riboswitch in a protein coding region." RNA 14, no. 12 (October 24, 2008): 2498–503. http://dx.doi.org/10.1261/rna.1269008.

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Guennewig, B., M. Roos, A. M. Dogar, L. F. R. Gebert, J. A. Zagalak, V. Vongrad, K. J. Metzner, and J. Hall. "Synthetic pre-microRNAs reveal dual-strand activity of miR-34a on TNF-." RNA 20, no. 1 (November 18, 2013): 61–75. http://dx.doi.org/10.1261/rna.038968.113.

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Stevens, A. "mRNA-decapping enzyme from Saccharomyces cerevisiae: purification and unique specificity for long RNA chains." Molecular and Cellular Biology 8, no. 5 (May 1988): 2005–10. http://dx.doi.org/10.1128/mcb.8.5.2005-2010.1988.

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An enzyme that hydrolyzes one PPi bond of the cap structure of mRNA, yielding m7GDP and 5'-p RNA was purified from Saccharomyces cerevisiae to a stage suitable for characterization. The specificity of the enzyme was studied, using both yeast mRNA and synthetic RNAs labeled in the cap structure. A synthetic capped RNA (540 nucleotides) was not reduced in size, while as much as 80% was decapped. Yeast mRNA treated with high concentrations of RNase A, nuclease P1, or micrococcal nuclease was inactive as a substrate. The use of synthetic capped RNAs of different sizes (50 to 540 nucleotides) as substrates showed that the larger RNA can be a better substrate by as much as 10-fold. GpppG-RNA was hydrolyzed at a rate similar to that at which 5'-triphosphate end group were not hydrolyzed.

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Kabza, Adam M., Brian E. Young, Nandini Kundu, and Jonathan T. Sczepanski. "Heterochiral nucleic acid circuits." Emerging Topics in Life Sciences 3, no. 5 (August 28, 2019): 501–6. http://dx.doi.org/10.1042/etls20190102.

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The programmability of DNA/RNA-based molecular circuits provides numerous opportunities in the field of synthetic biology. However, the stability of nucleic acids remains a major concern when performing complex computations in biological environments. Our solution to this problem is l-(deoxy)ribose nucleic acids (l-DNA/RNA), which are mirror images (i.e. enantiomers) of natural d-nucleotides. l-oligonucleotides have the same physical and chemical properties as their natural counterparts, yet they are completely invisible to the stereospecific environment of biology. We recently reported a novel strand-displacement methodology for transferring sequence information between oligonucleotide enantiomers (which are incapable of base pairing with each other), enabling bio-orthogonal l-DNA/RNA circuits to be easily interfaced with living systems. In this perspective, we summarize these so-called ‘heterochiral’ circuits, provide a viewpoint on their potential applications in synthetic biology, and discuss key problems that must be solved before achieving the ultimate goal of the engineering complex and reliable functionality.

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Rublack, Nico, Hien Nguyen, Bettina Appel, Danilo Springstubbe, Denise Strohbach, and Sabine Müller. "Synthesis of Specifically Modified Oligonucleotides for Application in Structural and Functional Analysis of RNA." Journal of Nucleic Acids 2011 (2011): 1–19. http://dx.doi.org/10.4061/2011/805253.

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Nowadays, RNA synthesis has become an essential tool not only in the field of molecular biology and medicine, but also in areas like molecular diagnostics and material sciences. Beyond synthetic RNAs for antisense, aptamer, ribozyme, and siRNA technologies, oligoribonucleotides carrying site-specific modifications for structure and function studies are needed. This often requires labeling of the RNA with a suitable spectroscopic reporter group. Herein, we describe the synthesis of functionalized monomer building blocks that upon incorporation in RNA allow for selective reaction with a specific reporter or functional entity. In particular, we report on the synthesis of 5′-O-dimethoxytrityl-2′-O-tert-butyldimethylsilyl protected 3′-O-phosphoramidites of nucleosides that carry amino linkers of different lengths and flexibility at the heterocyclic base, their incorporation in a variety of RNAs, and postsynthetic conjugation with fluorescent dyes and nitroxide spin labels. Further, we show the synthesis of a flavine mononucleotide-N-hydroxy-succinimidyl ester and its conjugation to amino functionalized RNA.

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English, Max A., Raphaël V. Gayet, and James J. Collins. "Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond." Annual Review of Biochemistry 90, no. 1 (June 20, 2021): 221–44. http://dx.doi.org/10.1146/annurev-biochem-013118-111914.

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In 1961, Jacob and Monod proposed the operon model of gene regulation. At the model's core was the modular assembly of regulators, operators, and structural genes. To illustrate the composability of these elements, Jacob and Monod linked phenotypic diversity to the architectures of regulatory circuits. In this review, we examine how the circuit blueprints imagined by Jacob and Monod laid the foundation for the first synthetic gene networks that launched the field of synthetic biology in 2000. We discuss the influences of the operon model and its broader theoretical framework on the first generation of synthetic biological circuits, which were predominantly transcriptional and posttranscriptional circuits. We also describe how recent advances in molecular biology beyond the operon model—namely, programmable DNA- and RNA-binding molecules as well as models of epigenetic and posttranslational regulation—are expanding the synthetic biology toolkit and enabling the design of more complex biological circuits.

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Dohno, Chikara, and Kazuhiko Nakatani. "Molecular Glue for RNA: Regulating RNA Structure and Function through Synthetic RNA Binding Molecules." ChemBioChem 20, no. 23 (September 20, 2019): 2903–10. http://dx.doi.org/10.1002/cbic.201900223.

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Gallivan, Justin P. "RNA Synthetic Biology: From the Test Tube to Cells and Back Again." ACS Synthetic Biology 4, no. 5 (May 15, 2015): 493–94. http://dx.doi.org/10.1021/acssynbio.5b00084.

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Hadd, Andrew, and John J. Perona. "Recoding Aminoacyl-tRNA Synthetases for Synthetic Biology by Rational Protein-RNA Engineering." ACS Chemical Biology 9, no. 12 (October 31, 2014): 2761–66. http://dx.doi.org/10.1021/cb5006596.

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Nshogozabahizi, J. C., K. L. Aubrey, J. A. Ross, and N. Thakor. "Applications and limitations of regulatory RNA elements in synthetic biology and biotechnology." Journal of Applied Microbiology 127, no. 4 (April 29, 2019): 968–84. http://dx.doi.org/10.1111/jam.14270.

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Wunnicke, D., D. Strohbach, J. E. Weigand, B. Appel, E. Feresin, B. Suess, S. Muller, and H. J. Steinhoff. "Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR." RNA 17, no. 1 (November 19, 2010): 182–88. http://dx.doi.org/10.1261/rna.2222811.

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DOWER, K. "A synthetic A tail rescues yeast nuclear accumulation of a ribozyme-terminated transcript." RNA 10, no. 12 (December 1, 2004): 1888–99. http://dx.doi.org/10.1261/rna.7166704.

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Stark, M. R., J. A. Pleiss, M. Deras, S. A. Scaringe, and S. D. Rader. "An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs." RNA 12, no. 11 (September 27, 2006): 2014–19. http://dx.doi.org/10.1261/rna.93506.

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Tizei, Pedro A. G., Eszter Csibra, Leticia Torres, and Vitor B. Pinheiro. "Selection platforms for directed evolution in synthetic biology." Biochemical Society Transactions 44, no. 4 (August 15, 2016): 1165–75. http://dx.doi.org/10.1042/bst20160076.

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Abstract:

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules–gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function–be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code.

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Feng, Xiaofan, and Mario Andrea Marchisio. "Saccharomyces cerevisiae Promoter Engineering before and during the Synthetic Biology Era." Biology 10, no. 6 (June 6, 2021): 504. http://dx.doi.org/10.3390/biology10060504.

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Synthetic gene circuits are made of DNA sequences, referred to as transcription units, that communicate by exchanging proteins or RNA molecules. Proteins are, mostly, transcription factors that bind promoter sequences to modulate the expression of other molecules. Promoters are, therefore, key components in genetic circuits. In this review, we focus our attention on the construction of artificial promoters for the yeast S. cerevisiae, a popular chassis for gene circuits. We describe the initial techniques and achievements in promoter engineering that predated the start of the Synthetic Biology epoch of about 20 years. We present the main applications of synthetic promoters built via different methods and discuss the latest innovations in the wet-lab engineering of novel promoter sequences.

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Balint, Eva, and Ildiko Unk. "Selective Metal Ion Utilization Contributes to the Transformation of the Activity of Yeast Polymerase η from DNA Polymerization toward RNA Polymerization." International Journal of Molecular Sciences 21, no. 21 (November 4, 2020): 8248. http://dx.doi.org/10.3390/ijms21218248.

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Polymerase eta (Polη) is a translesion synthesis DNA polymerase directly linked to cancer development. It can bypass several DNA lesions thereby rescuing DNA damage-stalled replication complexes. We previously presented evidence implicating Saccharomyces cerevisiae Polη in transcription elongation, and identified its specific RNA extension and translesion RNA synthetic activities. However, RNA synthesis by Polη proved rather inefficient under conditions optimal for DNA synthesis. Searching for factors that could enhance its RNA synthetic activity, we have identified the divalent cation of manganese. Here, we show that manganese triggers drastic changes in the activity of Polη. Kinetics experiments indicate that manganese increases the efficiency of ribonucleoside incorporation into RNA by ~400–2000-fold opposite undamaged DNA, and ~3000 and ~6000-fold opposite TT dimer and 8oxoG, respectively. Importantly, preference for the correct base is maintained with manganese during RNA synthesis. In contrast, activity is strongly impaired, and base discrimination is almost lost during DNA synthesis by Polη with manganese. Moreover, Polη shows strong preference for manganese during RNA synthesis even at a 25-fold excess magnesium concentration. Based on this, we suggest that a new regulatory mechanism, selective metal cofactor utilization, modulates the specificity of Polη helping it to perform distinct activities needed for its separate functions during replication and transcription.

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Osuji, Godson O., Jonas Konan, and Gitonga M’Mbijjewe. "RNA synthetic activity of glutamate dehydrogenase." Applied Biochemistry and Biotechnology 119, no. 3 (December 2004): 209–28. http://dx.doi.org/10.1007/s12010-004-0003-z.

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Journal articles on the topic 'RNA synthetic biology'

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