Frameworks for Programming RNA Devices

[1]  K Taira,et al.  A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the trans‐activation by Tat of transcription in vitro and in vivo , 2000, Genes to cells : devoted to molecular & cellular mechanisms.

[2]  Y. Kyōgoku,et al.  Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. , 1999, Genes & development.

[3]  J. Gallivan,et al.  Guiding bacteria with small molecules and RNA. , 2007, Journal of the American Chemical Society.

[4]  R. Breaker,et al.  Engineering precision RNA molecular switches. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Markus Wieland,et al.  Improved aptazyme design and in vivo screening enable riboswitching in bacteria. , 2008, Angewandte Chemie.

[6]  Farren J. Isaacs,et al.  Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.

[7]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[8]  Y. Yokobayashi,et al.  Reengineering a natural riboswitch by dual genetic selection. , 2007, Journal of the American Chemical Society.

[9]  N. Vaish,et al.  Isolation of hammerhead ribozymes with altered core sequences by in vitro selection. , 1997, Biochemistry.

[10]  Laising Yen,et al.  Engineering high-speed allosteric hammerhead ribozymes , 2007, Biological chemistry.

[11]  R. Hartmann,et al.  Selection of Hammerhead Ribozyme Variants with Low Mg2+ Requirement: Importance of Stem‐Loop II , 2002, Chembiochem : a European journal of chemical biology.

[12]  Farren J. Isaacs,et al.  RNA synthetic biology , 2006, Nature Biotechnology.

[13]  Zasha Weinberg,et al.  A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression , 2004, Science.

[14]  R. Breaker,et al.  Control of alternative RNA splicing and gene expression by eukaryotic riboswitches , 2007, Nature.

[15]  David R. Liu,et al.  In vivo evolution of an RNA-based transcriptional activator. , 2003, Chemistry & biology.

[16]  Michael Musheev,et al.  Nonequilibrium capillary electrophoresis of equilibrium mixtures: a universal tool for development of aptamers. , 2005, Journal of the American Chemical Society.

[17]  Barbara Fink,et al.  Conditional gene expression by controlling translation with tetracycline-binding aptamers. , 2003, Nucleic acids research.

[18]  Atsushi Ogawa,et al.  An Artificial Aptazyme‐Based Riboswitch and its Cascading System in E. coli , 2008, Chembiochem : a European journal of chemical biology.

[19]  Torsten Waldminghaus,et al.  Generation of synthetic RNA-based thermosensors , 2008, Biological chemistry.

[20]  Andrew D Ellington,et al.  Group I aptazymes as genetic regulatory switches , 2002, BMC biotechnology.

[21]  David Baker,et al.  Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.

[22]  W. Scott,et al.  Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis , 2006, Cell.

[23]  Isoform-specific 3'-untranslated sequences sort alpha-cardiac and beta- cytoplasmic actin messenger RNAs to different cytoplasmic compartments [published erratum appears in J Cell Biol 1993 Dec;123(6 Pt 2):following 1907] , 1993, The Journal of cell biology.

[24]  Jerry Pelletier,et al.  Inhibition of translation by RNA-small molecule interactions. , 2002, RNA.

[25]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[26]  Satoshi Nishikawa,et al.  Inhibition of HCV NS3 protease by RNA aptamers in cells. , 2003, Nucleic acids research.

[27]  J. Keasling,et al.  Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization. , 2001, Metabolic engineering.

[28]  James J. Collins,et al.  A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells , 2007, Cell.

[29]  Georg Sczakiel,et al.  Endogenous expression of a high-affinity pseudoknot RNA aptamer suppresses replication of HIV-1. , 2002, Nucleic acids research.

[30]  Shana Topp,et al.  Random Walks to Synthetic Riboswitches—A High‐Throughput Selection Based on Cell Motility , 2008, Chembiochem : a European journal of chemical biology.

[31]  D. Patel,et al.  Adaptive recognition by nucleic acid aptamers. , 2000, Science.

[32]  Chase L. Beisel,et al.  Design Principles for Riboswitch Function , 2009, PLoS Comput. Biol..

[33]  M. Berezovski,et al.  Selection of smart aptamers by equilibrium capillary electrophoresis of equilibrium mixtures (ECEEM). , 2005, Journal of the American Chemical Society.

[34]  S. K. Desai,et al.  Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. , 2004, Journal of the American Chemical Society.

[35]  Kirsten L. Frieda,et al.  Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers , 2008, Science.

[36]  Travis S. Bayer,et al.  Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.

[37]  Eric D Brown,et al.  A FACS‐Based Approach to Engineering Artificial Riboswitches , 2008, Chembiochem : a European journal of chemical biology.

[38]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[39]  Chase L. Beisel,et al.  Model-guided design of ligand-regulated RNAi for programmable control of gene expression , 2008, Molecular systems biology.

[40]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[41]  Sunjoo Jeong,et al.  Inhibition of the functions of the nucleocapsid protein of human immunodeficiency virus-1 by an RNA aptamer. , 2004, Biochemical and biophysical research communications.

[42]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[43]  H. Hennecke,et al.  A mRNA-based thermosensor controls expression of rhizobial heat shock genes. , 2001, Nucleic acids research.

[44]  Beatrix Suess,et al.  Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast , 2007, Nucleic acids research.

[45]  Ali Nahvi,et al.  An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.

[46]  J. Rossi,et al.  mRNA localization signals can enhance the intracellular effectiveness of hammerhead ribozymes. , 1999, RNA.

[47]  David H Mathews,et al.  Revolutions in RNA secondary structure prediction. , 2006, Journal of molecular biology.

[48]  R. Tsien,et al.  Aptamers switch on fluorescence of triphenylmethane dyes. , 2003, Journal of the American Chemical Society.

[49]  J. Gallivan,et al.  A flow cytometry-based screen for synthetic riboswitches , 2008, Nucleic acids research.

[50]  F. Nagawa,et al.  Control of gene expression by artificial introns in Saccharomyces cerevisiae. , 1989, Science.

[51]  Ronald R. Breaker,et al.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.

[52]  T. Lockett,et al.  Selected classes of minimised hammerhead ribozyme have very high cleavage rates at low Mg2+ concentration. , 1999, Nucleic acids research.

[53]  R. Breaker,et al.  Control of gene expression by a natural metabolite-responsive ribozyme , 2004, Nature.

[54]  Shana Topp,et al.  Riboswitches in unexpected places--a synthetic riboswitch in a protein coding region. , 2008, RNA.

[55]  David R. Liu,et al.  Engineering a ligand-dependent RNA transcriptional activator. , 2004, Chemistry & biology.

[56]  T. Hazelrigg The Destinies and Destinations of RNAs , 1998, Cell.

[57]  Alexander Revzin,et al.  Modulating endogenous gene expression of mammalian cells via RNA-small molecule interaction. , 2008, Biochemical and biophysical research communications.

[58]  S. K. Desai,et al.  A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. , 2007, Chemistry & biology.

[59]  M. Famulok,et al.  Intramers as promising new tools in functional proteomics. , 2001, Chemistry & biology.

[60]  Brian F. Pfleger,et al.  Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes , 2006, Nature Biotechnology.

[61]  Tanja Kortemme,et al.  Computational design of protein-protein interactions. , 2004, Current opinion in chemical biology.

[62]  Yohei Yokobayashi,et al.  Engineering complex riboswitch regulation by dual genetic selection. , 2008, Journal of the American Chemical Society.

[63]  D. Endy Foundations for engineering biology , 2005, Nature.

[64]  B. Suess,et al.  A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. , 2004, Nucleic acids research.

[65]  T. Inada,et al.  Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. , 2005, Genes & development.

[66]  R. Breaker,et al.  Gene regulation by riboswitches , 2004, Nature Reviews Molecular Cell Biology.

[67]  Maung Nyan Win,et al.  Frameworks for programming biological function through RNA parts and devices. , 2009, Chemistry & biology.

[68]  R. Weiss,et al.  A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.

[69]  Christina D. Smolke,et al.  Coordinated, Differential Expression of Two Genes through Directed mRNA Cleavage and Stabilization by Secondary Structures , 2000, Applied and Environmental Microbiology.

[70]  L. Cassiday,et al.  In vivo recognition of an RNA aptamer by its transcription factor target. , 2001, Biochemistry.

[71]  Yohei Yokobayashi,et al.  Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. , 2006, RNA.

[72]  E. Lai RNA Sensors and Riboswitches: Self-Regulating Messages , 2003, Current Biology.

[73]  Jeffrey E. Barrick,et al.  Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions , 2006, Science.

[74]  F. Major,et al.  The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.

[75]  Letha J. Sooter,et al.  Automated acquisition of aptamer sequences. , 2002, Combinatorial chemistry & high throughput screening.

[76]  M. Green,et al.  Controlling gene expression in living cells through small molecule-RNA interactions. , 1998, Science.

[77]  B. Suess,et al.  Engineered riboswitches: Overview, problems and trends , 2008, RNA biology.

[78]  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.

[79]  Juliane Neupert,et al.  Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli , 2008, Nucleic acids research.

[80]  C. Wilson,et al.  Laser-mediated, site-specific inactivation of RNA transcripts. , 1999, Proceedings of the National Academy of Sciences of the United States of America.