Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review
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Ron Weiss | R. Weiss | N. Sanders | Oliwia Andries | T. Kitada | K. Bodner | Tasuku Kitada | Niek N Sanders | Oliwia Andries | Katie Bodner | Ron Weiss
[1] A. Serganov,et al. A Decade of Riboswitches , 2013, Cell.
[2] Dobb's journal staff. Of interest , 2001, Administration in mental health.
[3] Michael Basler,et al. Immunodominance of an Antiviral Cytotoxic T Cell Response Is Shaped by the Kinetics of Viral Protein Expression1 , 2003, The Journal of Immunology.
[4] K. Lundstrom. Alphavirus-Based Vaccines. , 2016, Methods in molecular biology.
[5] Philip C. Bevilacqua,et al. Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation , 2010, Nucleic acids research.
[6] Ben Turner,et al. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. , 2005, RNA.
[7] Beatrix Suess,et al. Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast , 2007, Nucleic acids research.
[8] Steven J. Seedhouse,et al. Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules. , 2010, Angewandte Chemie.
[9] Beatrix Suess,et al. Screening for engineered neomycin riboswitches that control translation initiation. , 2007, RNA.
[10] R. Sachidanandam,et al. An in vivo RNAi screening approach to identify host determinants of virus replication. , 2013, Cell host & microbe.
[11] T. Wandless,et al. A general chemical method to regulate protein stability in the mammalian central nervous system. , 2010, Chemistry & biology.
[12] Christina D Smolke,et al. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. , 2012, Current opinion in biotechnology.
[13] A. Muotri,et al. Efficient generation of human iPSCs by a synthetic self-replicative RNA. , 2013, Cell stem cell.
[14] Hirohide Saito,et al. Synthetic human cell fate regulation by protein-driven RNA switches , 2011, Nature Communications.
[15] Ian Small,et al. The potential for manipulating RNA with pentatricopeptide repeat proteins. , 2014, The Plant journal : for cell and molecular biology.
[16] E. Luman,et al. The need for innovative strategies to improve immunisation services in rural Zimbabwe. , 2012, Disasters.
[17] J. Szostak,et al. In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.
[18] E. Westhof,et al. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity , 2003, Nature Structural Biology.
[19] K. Dery,et al. Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing , 2008, BMC Molecular Biology.
[20] L. Gold,et al. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.
[21] Yohei Yokobayashi,et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. , 2006, RNA.
[22] C. Barreau,et al. Tethering of proteins to RNAs by bacteriophage proteins , 2008, Biology of the cell.
[23] Martin Fussenegger,et al. From gene switches to mammalian designer cells: present and future prospects. , 2013, Trends in biotechnology.
[24] Alexander Meissner,et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. , 2010, Cell stem cell.
[25] K. Lundstrom. Alphavirus-Based Vaccines , 2002, Viruses.
[26] Beatrix Suess,et al. Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity , 2010, Nucleic acids research.
[27] Christopher A. Voigt,et al. Principles of genetic circuit design , 2014, Nature Methods.
[28] Tomoaki Hara,et al. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. , 2010, Nature chemical biology.
[29] Steven J. Seedhouse,et al. Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside–RNA hairpin loop interactions , 2009, Nucleic acids research.
[30] Markus Wieland,et al. Rational design of a small molecule-responsive intramer controlling transgene expression in mammalian cells , 2011, Nucleic acids research.
[31] Byoung-Tak Zhang,et al. Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex , 2006, Cell.
[32] D. Weissman,et al. Nucleoside modifications in RNA limit activation of 2′-5′-oligoadenylate synthetase and increase resistance to cleavage by RNase L , 2011, Nucleic acids research.
[33] Martin Fussenegger,et al. Reward-based hypertension control by a synthetic brain–dopamine interface , 2013, Proceedings of the National Academy of Sciences.
[34] M. Gossen,et al. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[35] Yohei Yokobayashi,et al. Combinatorially inducible RNA interference triggered by chemically modified oligonucleotides. , 2011, Journal of the American Chemical Society.
[36] John J. Rossi,et al. Cell-type-specific, Aptamer-functionalized Agents for Targeted Disease Therapy , 2014, Molecular therapy. Nucleic acids.
[37] J. Doudna,et al. Molecular mechanisms of RNA interference. , 2013, Annual review of biophysics.
[38] Chase L. Beisel,et al. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing , 2010, Nucleic acids research.
[39] Karl-Dieter Entian,et al. A fast and efficient translational control system for conditional expression of yeast genes , 2009, Nucleic acids research.
[40] Christina D Smolke,et al. Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins , 2010, Science.
[41] M. Win,et al. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function , 2007, Proceedings of the National Academy of Sciences.
[42] J. Rosenecker,et al. Expression of therapeutic proteins after delivery of chemically modified mRNA in mice , 2011, Nature Biotechnology.
[43] Matthew D Disney,et al. Two-dimensional combinatorial screening identifies specific aminoglycoside-RNA internal loop partners. , 2008, Journal of the American Chemical Society.
[44] R. Stoltenburg,et al. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. , 2007, Biomolecular engineering.
[45] Yang Wang,et al. Engineering RNA Endonucleases with Customized Sequence Specificities , 2012, Nature Communications.
[46] N. Sonenberg,et al. Principles of translational control: an overview. , 2012, Cold Spring Harbor perspectives in biology.
[47] J. H. Strauss,et al. The Alphaviruses: Gene Expression, Replication, and Evolution , 1994, Microbiological reviews.
[48] Carola Engler,et al. A One Pot, One Step, Precision Cloning Method with High Throughput Capability , 2008, PloS one.
[49] J. Burnett,et al. RNA-based therapeutics: current progress and future prospects. , 2012, Chemistry & biology.
[50] D. Schaffer,et al. Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. , 2014, Angewandte Chemie.
[51] Barbara Fink,et al. Conditional gene expression by controlling translation with tetracycline-binding aptamers. , 2003, Nucleic acids research.
[52] B. Suess,et al. Mechanistic Basis for RNA Aptamer‐Based Induction of TetR , 2011, Chembiochem : a European journal of chemical biology.
[53] R. Gaur,et al. An artificial riboswitch for controlling pre-mRNA splicing. , 2005, RNA.
[54] M. Wickens,et al. Targeted translational regulation using the PUF protein family scaffold , 2011, Proceedings of the National Academy of Sciences.
[55] L. Naldini,et al. Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer , 2006, Nature Medicine.
[56] Christina D Smolke,et al. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems , 2010, Proceedings of the National Academy of Sciences.
[57] Martin Fussenegger,et al. Pharmaceutically controlled designer circuit for the treatment of the metabolic syndrome , 2012, Proceedings of the National Academy of Sciences.
[58] E. Gilboa,et al. Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay , 2010, Nature.
[59] Yen-Hsiang Wang,et al. Synthetic biology: advancing the design of diverse genetic systems. , 2013, Annual review of chemical and biomolecular engineering.
[60] Jon R Lorsch,et al. The mechanism of eukaryotic translation initiation: new insights and challenges. , 2012, Cold Spring Harbor perspectives in biology.
[61] Brian J. Belmont,et al. Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction , 2012, PloS one.
[62] Brian J. Belmont,et al. Engineering a direct and inducible protein-RNA interaction to regulate RNA biology. , 2010, ACS chemical biology.
[63] Hirohide Saito,et al. A versatile cis-acting inverter module for synthetic translational switches , 2013, Nature Communications.
[64] R. Weiss,et al. Foundations for the design and implementation of synthetic genetic circuits , 2012, Nature Reviews Genetics.
[65] Aleksandra Filipovska,et al. A universal code for RNA recognition by PUF proteins. , 2011, Nature chemical biology.
[66] Zhen Xie,et al. Logic integration of mRNA signals by an RNAi-based molecular computer , 2010, Nucleic acids research.
[67] Hiroki Kato,et al. Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.
[68] Yohei Yokobayashi,et al. Conditional RNA interference mediated by allosteric ribozyme. , 2009, Journal of the American Chemical Society.
[69] L. Peelman,et al. Innate immune response and programmed cell death following carrier-mediated delivery of unmodified mRNA to respiratory cells. , 2013, Journal of controlled release : official journal of the Controlled Release Society.
[70] Steven M. Gallo,et al. Sequence-based design of bioactive small molecules that target precursor microRNAs , 2014, Nature chemical biology.
[71] T. Wandless,et al. Destabilizing domains derived from the human estrogen receptor. , 2012, Journal of the American Chemical Society.
[72] Luc Jaeger,et al. RNA modularity for synthetic biology , 2013, F1000prime reports.
[73] Roger Y Tsien,et al. Control of mammalian translation by mRNA structure near caps. , 2006, RNA.
[74] Jacob J. Hughey,et al. High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells , 2014, Cell.
[75] Huimin Zhao,et al. Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA , 2014, Journal of biological engineering.
[76] Özlem Türeci,et al. mRNA-based therapeutics — developing a new class of drugs , 2014, Nature Reviews Drug Discovery.
[77] Daniel G. Anderson,et al. Non-viral vectors for gene-based therapy , 2014, Nature Reviews Genetics.
[78] L. Peelman,et al. Comparison of the gene transfer efficiency of mRNA/GL67 and pDNA/GL67 complexes in respiratory cells. , 2012, Molecular Pharmaceutics.
[79] Jerry Pelletier,et al. Inhibition of translation by RNA-small molecule interactions. , 2002, RNA.
[80] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[81] K. White,et al. Higher-Order RNA Structural Requirements and Small-Molecule Induction of Tombusvirus Subgenomic mRNA Transcription , 2008, Journal of Virology.
[82] Y. Liu,et al. Structural basis for the modular recognition of single-stranded RNA by PPR proteins , 2013, Nature.
[83] P. Rod Dunbar,et al. Competition Between CTL Narrows the Immune Response Induced by Prime-Boost Vaccination Protocols1 , 2002, The Journal of Immunology.
[84] Simon Ausländer,et al. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. , 2010, Molecular bioSystems.
[85] Stijn van Dongen,et al. miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..
[86] James A. Stapleton,et al. Quantitative and simultaneous translational control of distinct mammalian mRNAs , 2013, Nucleic acids research.
[87] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[88] S. Almo,et al. Aptamer-targeted Antigen Delivery , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.
[89] F. Zepp. Principles of vaccine design-Lessons from nature. , 2010, Vaccine.
[90] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[91] H. Park,et al. High Cleavage Efficiency of a 2A Peptide Derived from Porcine Teschovirus-1 in Human Cell Lines, Zebrafish and Mice , 2011, PloS one.
[92] Thomas Krucker,et al. Nonviral delivery of self-amplifying RNA vaccines , 2012, Proceedings of the National Academy of Sciences.
[93] A. Ferré-D’Amaré,et al. Small self-cleaving ribozymes. , 2010, Cold Spring Harbor perspectives in biology.
[94] Yang Wang,et al. Engineering splicing factors with designed specificities , 2009, Nature Methods.
[95] Martin Fussenegger,et al. Synthetic mammalian gene circuits for biomedical applications. , 2013, Current opinion in chemical biology.
[96] R. Weiss,et al. A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.
[97] C. Contag,et al. Chemical control of protein stability and function in living mice , 2008, Nature Medicine.
[98] M. Gossen,et al. Transcriptional activation by tetracyclines in mammalian cells. , 1995, Science.
[99] William I. Bacchus,et al. Biomedically relevant circuit-design strategies in mammalian synthetic biology , 2013, Molecular systems biology.
[100] Charles S. Bond,et al. A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins , 2012, PLoS genetics.
[101] Houping Ni,et al. Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. , 2005, Immunity.
[102] Martin Fussenegger,et al. A designer cell-based histamine-specific human allergy profiler , 2014, Nature Communications.
[103] R R Breaker,et al. Rational design of allosteric ribozymes. , 1997, Chemistry & biology.
[104] Zhen Xie,et al. Rationally-designed logic integration of regulatory signals in mammalian cells , 2010, Nature nanotechnology.
[105] G. Vanham,et al. Challenges and advances towards the rational design of mRNA vaccines. , 2013, Trends in molecular medicine.
[106] Corey W. Liu,et al. Small molecule displacement of a cryptic degron causes conditional protein degradation , 2011, Nature chemical biology.
[107] Yaakov Benenson,et al. Synthetic biology with RNA: progress report. , 2012, Current opinion in chemical biology.
[108] M. Win,et al. Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.
[109] Brian J. Belmont,et al. Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction , 2012, Nucleic acids research.
[110] Jacob Beal,et al. Model-driven engineering of gene expression from RNA replicons. , 2015, ACS synthetic biology.
[111] S. Pascolo. Vaccination with messenger RNA (mRNA). , 2008, Handbook of experimental pharmacology.
[112] Atsushi Ogawa,et al. Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors. , 2011, RNA.
[113] T. Lithgow,et al. PUF proteins: repression, activation and mRNA localization. , 2011, Trends in cell biology.
[114] L. Banaszynski,et al. A Rapid, Reversible, and Tunable Method to Regulate Protein Function in Living Cells Using Synthetic Small Molecules , 2006, Cell.
[115] E. Maxwell,et al. Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif. , 2010, RNA.
[116] T. Hall. Expanding the RNA-recognition code of PUF proteins , 2014, Nature Structural &Molecular Biology.
[117] Zhijian J. Chen,et al. SnapShot: Pathways of Antiviral Innate Immunity , 2010, Cell.
[118] Yohei Yokobayashi,et al. Controlling Mammalian Gene Expression by Allosteric Hepatitis Delta Virus Ribozymes , 2013, ACS synthetic biology.
[119] D. Walsh,et al. Tinkering with translation: protein synthesis in virus-infected cells. , 2013, Cold Spring Harbor perspectives in biology.
[120] M. Elowitz,et al. Synthetic Biology: Integrated Gene Circuits , 2011, Science.
[121] H. Sugiyama,et al. Engineering RNA-protein complexes with different shapes for imaging and therapeutic applications. , 2014, ACS nano.
[122] Phillip D. Zamore,et al. Modular Recognition of RNA by a Human Pumilio-Homology Domain , 2002, Cell.
[123] M. Hentze,et al. Proteins binding to 5' untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells , 1994, Molecular and cellular biology.
[124] Martin Fussenegger,et al. A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. , 2014, Molecular cell.
[125] Y. Benenson. RNA-based computation in live cells. , 2009, Current opinion in biotechnology.
[126] A protein-RNA specificity code enables targeted activation of an endogenous human transcript , 2014, Nature Structural &Molecular Biology.
[127] A. Hüttenhofer,et al. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. , 2003, Nucleic acids research.
[128] Farren J. Isaacs,et al. RNA synthetic biology , 2006, Nature Biotechnology.
[129] A. Ogawa. Ligand‐Dependent Upregulation of Ribosomal Shunting , 2013, Chembiochem : a European journal of chemical biology.
[130] G. Leroux-Roels,et al. Unmet needs in modern vaccinology: adjuvants to improve the immune response. , 2010, Vaccine.
[131] Florian Groher,et al. Synthetic riboswitches - A tool comes of age. , 2014, Biochimica et biophysica acta.
[132] Oberdan Leo,et al. Key concepts in immunology. , 2010, Vaccine.
[133] Günter Mayer,et al. An RNA aptamer that induces transcription. , 2009, Chemistry & biology.
[134] F. Lienert,et al. Synthetic biology in mammalian cells: next generation research tools and therapeutics , 2014, Nature Reviews Molecular Cell Biology.
[135] Travis S. Bayer,et al. Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.
[136] D. Dean,et al. Progress and prospects: nuclear import of nonviral vectors , 2010, Gene Therapy.
[137] M. Green,et al. Controlling gene expression in living cells through small molecule-RNA interactions. , 1998, Science.
[138] C. Mandl,et al. RNA: the new revolution in nucleic acid vaccines. , 2013, Seminars in immunology.
[139] R. Albrecht,et al. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies , 2013, Nature Biotechnology.
[140] Martin Fussenegger,et al. Self-sufficient control of urate homeostasis in mice by a synthetic circuit , 2010, Nature Biotechnology.
[141] Barbara Fink,et al. Tetracycline‐aptamer‐mediated translational regulation in yeast , 2003, Molecular microbiology.
[142] Hirohide Saito,et al. Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation , 2012, Nucleic acids research.
[143] Markus Wieland,et al. Programmable single-cell mammalian biocomputers , 2012, Nature.
[144] Margaret S. Ebert,et al. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells , 2007, Nature Methods.
[145] James A. Stapleton,et al. Feedback Control of Protein Expression in Mammalian Cells by Tunable Synthetic Translational Inhibition , 2011, ACS synthetic biology.
[146] Priscilla E. M. Purnick,et al. The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.
[147] K. Ljungberg,et al. Self-replicating alphavirus RNA vaccines , 2015, Expert review of vaccines.
[148] S. Yoshimura,et al. Synthetic RNA-protein complex shaped like an equilateral triangle. , 2011, Nature nanotechnology.