Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression
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Satya Prakash | Alfonso Jaramillo | Guillermo Rodrigo | Boris Kirov | Thomas E. Landrain | Eszter Majer | José-Antonio Daròs | G. Rodrigo | A. Jaramillo | S. Shen | S. Prakash | E. Majer | J. Daròs | B. Kirov | Shensi Shen | Shensi Shen
[1] Farren J. Isaacs,et al. RNA synthetic biology , 2006, Nature Biotechnology.
[2] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[3] Joe C. Liang,et al. Engineering biological systems with synthetic RNA molecules. , 2011, Molecular cell.
[4] Engineering modular protein interaction switches by sequence overlap. , 2007, Journal of the American Chemical Society.
[5] Travis S. Bayer,et al. Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.
[6] R. Breaker,et al. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes , 2005, Nature Biotechnology.
[7] D. Patel,et al. Adaptive recognition by nucleic acid aptamers. , 2000, Science.
[8] A. Pardi,et al. Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer. , 2000, RNA.
[9] Tanja Kortemme,et al. Computational design of protein-protein interactions. , 2004, Current opinion in chemical biology.
[10] Farren J. Isaacs,et al. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators , 2010, Proceedings of the National Academy of Sciences.
[11] Luke A. Gilbert,et al. CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.
[12] Rick Dale,et al. Assessing bimodality to detect the presence of a dual cognitive process , 2013, Behavior research methods.
[13] Christopher A. Voigt,et al. Ribozyme-based insulator parts buffer synthetic circuits from genetic context , 2012, Nature Biotechnology.
[14] W. Lim,et al. Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination , 2003, Science.
[15] C. Bashor,et al. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. , 2010, Annual review of biophysics.
[16] Tamar Schlick,et al. Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function , 2012, PLoS Comput. Biol..
[17] Adam P Arkin,et al. RNA processing enables predictable programming of gene expression , 2012, Nature Biotechnology.
[18] M. Elowitz,et al. Programming gene expression with combinatorial promoters , 2007, Molecular systems biology.
[19] James J. Collins,et al. Genetic switchboard for synthetic biology applications , 2012, Proceedings of the National Academy of Sciences.
[20] Wenjiao Song,et al. Fluorescence Imaging of Cellular Metabolites with RNA , 2012, Science.
[21] M. Stone,et al. In silico selection of RNA aptamers , 2009, Nucleic acids research.
[22] M. Bennett,et al. Microfluidic devices for measuring gene network dynamics in single cells , 2009, Nature Reviews Genetics.
[23] Luke E. Ulrich,et al. One-component systems dominate signal transduction in prokaryotes. , 2005, Trends in microbiology.
[24] J. Sambrook,et al. Molecular Cloning: A Laboratory Manual , 2001 .
[25] Xi Chen,et al. Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes , 2009, PLoS Comput. Biol..
[26] D. Bartel,et al. Isolation of new ribozymes from a large pool of random sequences [see comment]. , 1993, Science.
[27] Robert T Sauer,et al. SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[28] Farren J. Isaacs,et al. Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.
[29] L. Serrano,et al. Engineering Signal Transduction Pathways , 2010, Cell.
[30] H. Sambrook. Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .
[31] Ruth J. Williams,et al. Queueing up for Enzymatic Processing: Correlated Signaling through Coupled Degradation , 2022 .
[32] Steven M. Block,et al. Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination , 2008, Cell.
[33] H. Bujard,et al. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.
[34] Alfonso Jaramillo,et al. AutoBioCAD: full biodesign automation of genetic circuits. , 2013, ACS synthetic biology.
[35] Alfonso Jaramillo,et al. Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. , 2013, Chaos.
[36] Yann Ponty,et al. VARNA: Interactive drawing and editing of the RNA secondary structure , 2009, Bioinform..
[37] G. Hong,et al. Nucleic Acids Research , 2015, Nucleic Acids Research.
[38] T. Terwilliger,et al. Engineering and characterization of a superfolder green fluorescent protein , 2006, Nature Biotechnology.
[39] Wilson W Wong,et al. Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator , 2007, Molecular systems biology.
[40] Giovanni Bertoni,et al. One-step high-throughput assay for quantitative detection of beta-galactosidase activity in intact gram-negative bacteria, yeast, and mammalian cells. , 2006, BioTechniques.
[41] M. Green,et al. Controlling gene expression in living cells through small molecule-RNA interactions. , 1998, Science.
[42] L. Tsimring,et al. A synchronized quorum of genetic clocks , 2009, Nature.
[43] L. Looger,et al. Computational design of receptor and sensor proteins with novel functions , 2003, Nature.
[44] Benedikt Klauser,et al. An engineered small RNA-mediated genetic switch based on a ribozyme expression platform , 2013, Nucleic acids research.
[45] R. D'Amato,et al. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage , 2004, Nature.
[46] Julius B. Lucks,et al. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals , 2012, Nucleic acids research.
[47] Markus Wieland,et al. Artificial ribozyme switches containing natural riboswitch aptamer domains. , 2009, Angewandte Chemie.
[48] Thomas E. Landrain,et al. De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells , 2012, Proceedings of the National Academy of Sciences.
[49] Conrad Steenberg,et al. NUPACK: Analysis and design of nucleic acid systems , 2011, J. Comput. Chem..
[50] Luke A. Gilbert,et al. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.
[51] Adam P Arkin,et al. Supplementary information for Rationally designed families of orthogonal RNA regulators of translation , 2012 .
[52] References , 1971 .
[53] M. Bennett,et al. A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.
[54] Walter Fontana,et al. Fast folding and comparison of RNA secondary structures , 1994 .
[55] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[56] 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.
[57] Markus Wieland,et al. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. , 2008, Angewandte Chemie.
[58] Adam P Arkin,et al. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation , 2012, Nature Methods.
[59] Thomas E. Landrain,et al. A new frontier in synthetic biology: automated design of small RNA devices in bacteria. , 2013, Trends in genetics : TIG.