Frameworks for Programming Biological Function through RNA Parts and Devices
Tài liệu tham khảo
Alifano, 1994, Control of mRNA processing and decay in prokaryotes, Genetica, 94, 157, 10.1007/BF01443430
An, 2006, Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction, RNA, 12, 710, 10.1261/rna.2299306
Babendure, 2003, Aptamers switch on fluorescence of triphenylmethane dyes, J. Am. Chem. Soc., 125, 14716, 10.1021/ja037994o
Bassell, 1999, The travels of mRNAs through all cells large and small, FASEB J., 13, 447, 10.1096/fasebj.13.3.447
Basu, 2005, A synthetic multicellular system for programmed pattern formation, Nature, 434, 1130, 10.1038/nature03461
Beisel, 2008, Model-guided design of ligand-regulated RNAi for programmable control of gene expression, Mol. Syst. Biol., 4, 224, 10.1038/msb.2008.62
Berezovski, 2005, Nonequilibrium capillary electrophoresis of equilibrium mixtures: a universal tool for development of aptamers, J. Am. Chem. Soc., 127, 3165, 10.1021/ja042394q
Bernstein, 2001, Role for a bidentate ribonuclease in the initiation step of RNA interference, Nature, 409, 363, 10.1038/35053110
Blount, 2005, The structure-function dilemma of the hammerhead ribozyme, Annu. Rev. Biophys. Biomol. Struct., 34, 415, 10.1146/annurev.biophys.34.122004.184428
Bonoli, 2006, RNA complementary to the 5′ UTR of mRNA triggers effective silencing in Saccharomyces cerevisiae, Biochem. Biophys. Res. Commun., 339, 1224, 10.1016/j.bbrc.2005.11.137
Breaker, 2008, Complex riboswitches, Science, 319, 1795, 10.1126/science.1152621
Brown, 2007, Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state, Nat. Biotechnol., 25, 1457, 10.1038/nbt1372
Brummelkamp, 2002, A system for stable expression of short interfering RNAs in mammalian cells, Science, 296, 550, 10.1126/science.1068999
Bunch, 1989, The conditional inhibition of gene expression in cultured Drosophila cells by antisense RNA, Nucleic Acids Res., 17, 9761, 10.1093/nar/17.23.9761
Buskirk, 2003, In vivo evolution of an RNA-based transcriptional activator, Chem. Biol., 10, 533, 10.1016/S1074-5521(03)00109-1
Buskirk, 2004, Engineering a ligand-dependent RNA transcriptional activator, Chem. Biol., 11, 1157, 10.1016/j.chembiol.2004.05.017
Canton, 2008, Refinement and standardization of synthetic biological parts and devices, Nat. Biotechnol., 26, 787, 10.1038/nbt1413
Carrier, 1997, Controlling messenger RNA stability in bacteria: strategies for engineering gene expression, Biotechnol. Prog., 13, 699, 10.1021/bp970095h
Carrier, 1999, Library of synthetic 5′ secondary structures to manipulate mRNA stability in Escherichia coli, Biotechnol. Prog., 15, 58, 10.1021/bp9801143
Cassiday, 2001, In vivo recognition of an RNA aptamer by its transcription factor target, Biochemistry, 40, 2433, 10.1021/bi002376v
Chanfreau, 2000, Recognition of a conserved class of RNA tetraloops by Saccharomyces cerevisiae RNase III, Proc. Natl. Acad. Sci. USA, 97, 3142, 10.1073/pnas.97.7.3142
Chappell, 2000, A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity, Proc. Natl. Acad. Sci. USA, 97, 1536, 10.1073/pnas.97.4.1536
Chen, 1994, Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs, Nucleic Acids Res., 22, 4953, 10.1093/nar/22.23.4953
Coleman, 1984, The use of RNAs complementary to specific mRNAs to regulate the expression of individual bacterial genes, Cell, 37, 429, 10.1016/0092-8674(84)90373-8
Conaty, 1999, Selected classes of minimised hammerhead ribozyme have very high cleavage rates at low Mg2+ concentration, Nucleic Acids Res., 27, 2400, 10.1093/nar/27.11.2400
Cox, 2002, Automated acquisition of aptamer sequences, Comb. Chem. High Throughput Screen., 5, 289, 10.2174/1386207023330291
Crooke, 2004, Progress in antisense technology, Annu. Rev. Med., 55, 61, 10.1146/annurev.med.55.091902.104408
Deans, 2007, A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells, Cell, 130, 363, 10.1016/j.cell.2007.05.045
Desai, 2004, Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation, J. Am. Chem. Soc., 126, 13247, 10.1021/ja048634j
Doudna, 2002, The chemical repertoire of natural ribozymes, Nature, 418, 222, 10.1038/418222a
Drabovich, 2005, Selection of smart aptamers by equilibrium capillary electrophoresis of equilibrium mixtures (ECEEM), J. Am. Chem. Soc., 127, 11224, 10.1021/ja0530016
Dykxhoorn, 2003, Killing the messenger: short RNAs that silence gene expression, Nat. Rev. Mol. Cell Biol., 4, 457, 10.1038/nrm1129
Ellington, 1990, In vitro selection of RNA molecules that bind specific ligands, Nature, 346, 818, 10.1038/346818a0
Endy, 2005, Foundations for engineering biology, Nature, 438, 449, 10.1038/nature04342
Famulok, 2001, Intramers as promising new tools in functional proteomics, Chem. Biol., 8, 931, 10.1016/S1074-5521(01)00070-9
Fowler, 2008, A FACS-based approach to engineering artificial riboswitches, ChemBioChem, 9, 1906, 10.1002/cbic.200700713
Ge, 2005, RNase III-mediated silencing of a glucose-dependent repressor in yeast, Curr. Biol., 15, 140, 10.1016/j.cub.2004.12.001
Grate, 1999, Laser-mediated, site-specific inactivation of RNA transcripts, Proc. Natl. Acad. Sci. USA, 96, 6131, 10.1073/pnas.96.11.6131
Green, 1986, The role of antisense RNA in gene regulation, Annu. Rev. Biochem., 55, 569, 10.1146/annurev.bi.55.070186.003033
Greenleaf, 2008, Direct observation of hierarchical folding in single riboswitch aptamers, Science, 319, 630, 10.1126/science.1151298
Hammond, 2000, An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells, Nature, 404, 293, 10.1038/35005107
Harvey, 2002, Inhibition of translation by RNA-small molecule interactions, RNA, 8, 452, 10.1017/S135583820202633X
Hazelrigg, 1998, The destinies and destinations of RNAs, Cell, 95, 451, 10.1016/S0092-8674(00)81613-X
Hellen, 2001, Internal ribosome entry sites in eukaryotic mRNA molecules, Genes Dev., 15, 1593, 10.1101/gad.891101
Henkin, 2000, Transcription termination control in bacteria, Curr. Opin. Microbiol., 3, 149, 10.1016/S1369-5274(00)00067-9
Henkin, 2002, Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions, Bioessays, 24, 700, 10.1002/bies.10125
Hermann, 2000, Adaptive recognition by nucleic acid aptamers, Science, 287, 820, 10.1126/science.287.5454.820
Hutvagner, 2002, A microRNA in a multiple-turnover RNAi enzyme complex, Science, 297, 2056, 10.1126/science.1073827
Isaacs, 2006, RNA synthetic biology, Nat. Biotechnol., 24, 545, 10.1038/nbt1208
Isaacs, 2004, Engineered riboregulators enable post-transcriptional control of gene expression, Nat. Biotechnol., 22, 841, 10.1038/nbt986
Joyce, 2007, Forty years of in vitro evolution, Angew. Chem. Int. Ed. Engl., 46, 6420, 10.1002/anie.200701369
Khvorova, 2003, Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity, Nat. Struct. Biol., 10, 708, 10.1038/nsb959
Kieft, 2002, Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation, Nat. Struct. Biol., 9, 370
Kijima, 1998, Hammerhead ribozymes against gamma-glutamylcysteine synthetase mRNA down-regulate intracellular glutathione concentration of mouse islet cells, Biochem. Biophys. Res. Commun., 247, 697, 10.1006/bbrc.1998.8878
Kim, 2008, Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing, BMC Mol. Biol., 9, 23, 10.1186/1471-2199-9-23
Kim, 2004, Inhibition of the functions of the nucleocapsid protein of human immunodeficiency virus-1 by an RNA aptamer, Biochem. Biophys. Res. Commun., 320, 1181, 10.1016/j.bbrc.2004.06.077
Kislauskis, 1993, Isoform-specific 3′-untranslated sequences sort alpha-cardiac and beta-cytoplasmic actin messenger RNAs to different cytoplasmic compartments, J. Cell Biol., 123, 165, 10.1083/jcb.123.1.165
Kozak, 1999, Initiation of translation in prokaryotes and eukaryotes, Gene, 234, 187, 10.1016/S0378-1119(99)00210-3
Lai, 2003, RNA sensors and riboswitches: self-regulating messages, Curr. Biol., 13, R285, 10.1016/S0960-9822(03)00203-3
Lee, 1999, mRNA localization signals can enhance the intracellular effectiveness of hammerhead ribozymes, RNA, 5, 1200, 10.1017/S1355838299990246
Lee, 2003, The nuclear RNase III Drosha initiates microRNA processing, Nature, 425, 415, 10.1038/nature01957
Link, 2007, Engineering high-speed allosteric hammerhead ribozymes, Biol. Chem., 388, 779, 10.1515/BC.2007.105
Lund, 2004, Nuclear export of microRNA precursors, Science, 303, 95, 10.1126/science.1090599
Lundberg, 1990, Cleavages in the 5′ region of the ompA and bla mRNA control stability: studies with an E. coli mutant altering mRNA stability and a novel endoribonuclease, EMBO J., 9, 2731, 10.1002/j.1460-2075.1990.tb07460.x
Lynch, 2007, A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function, Chem. Biol., 14, 173, 10.1016/j.chembiol.2006.12.008
Lynch, 2009, A flow cytometry-based screen for synthetic riboswitches, Nucleic Acids Res., 37, 184, 10.1093/nar/gkn924
Mandal, 2004, Gene regulation by riboswitches, Nat. Rev. Mol. Cell Biol., 5, 451, 10.1038/nrm1403
Maniatis, 2002, Alternative pre-mRNA splicing and proteome expansion in metazoans, Nature, 418, 236, 10.1038/418236a
Martick, 2006, Tertiary contacts distant from the active site prime a ribozyme for catalysis, Cell, 126, 309, 10.1016/j.cell.2006.06.036
Mathews, 2006, Revolutions in RNA secondary structure prediction, J. Mol. Biol., 359, 526, 10.1016/j.jmb.2006.01.067
McDowall, 1994, A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage, J. Biol. Chem., 269, 10790, 10.1016/S0021-9258(17)34129-7
McManus, 2002, Gene silencing using micro-RNA designed hairpins, RNA, 8, 842, 10.1017/S1355838202024032
McNamara, 2006, Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras, Nat. Biotechnol., 24, 1005, 10.1038/nbt1223
Meaux, 2006, Yeast transcripts cleaved by an internal ribozyme provide new insight into the role of the cap and poly(A) tail in translation and mRNA decay, RNA, 12, 1323, 10.1261/rna.46306
Meister, 2004, Mechanisms of gene silencing by double-stranded RNA, Nature, 431, 343, 10.1038/nature02873
Miyagishi, 2002, U6 promoter-driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells, Nat. Biotechnol., 20, 497, 10.1038/nbt0502-497
Morino, 2000, Hammerhead ribozyme specifically inhibits vascular endothelial growth factor gene expression in a human hepatocellular carcinoma cell line, Int. J. Oncol., 17, 495
Narberhaus, 2006, RNA thermometers, FEMS Microbiol. Rev., 30, 3, 10.1111/j.1574-6976.2005.004.x
Neupert, 2008, Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli, Nucleic Acids Res., 36, e124, 10.1093/nar/gkn545
Nishikawa, 2003, Inhibition of HCV NS3 protease by RNA aptamers in cells, Nucleic Acids Res., 31, 1935, 10.1093/nar/gkg291
Nomura, 2007, Reengineering a natural riboswitch by dual genetic selection, J. Am. Chem. Soc., 129, 13814, 10.1021/ja076298b
Ogawa, 2008, An artificial aptazyme-based riboswitch and its cascading system in E. coli, ChemBioChem, 9, 206, 10.1002/cbic.200700478
Owens, 2001, Identification of two short internal ribosome entry sites selected from libraries of random oligonucleotides, Proc. Natl. Acad. Sci. USA, 98, 1471, 10.1073/pnas.98.4.1471
Parisien, 2008, The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, Nature, 452, 51, 10.1038/nature06684
Pawson, 1997, Signaling through scaffold, anchoring, and adaptor proteins, Science, 278, 2075, 10.1126/science.278.5346.2075
Pelletier, 1985, Insertion mutagenesis to increase secondary structure within the 5′ noncoding region of a eukaryotic mRNA reduces translational efficiency, Cell, 40, 515, 10.1016/0092-8674(85)90200-4
Pfleger, 2006, Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes, Nat. Biotechnol., 24, 1027, 10.1038/nbt1226
Rackham, 2005, A network of orthogonal ribosome x mRNA pairs, Nat. Chem. Biol., 1, 159, 10.1038/nchembio719
Reynolds, 2004, Rational siRNA design for RNA interference, Nat. Biotechnol., 22, 326, 10.1038/nbt936
Rinaudo, 2007, A universal RNAi-based logic evaluator that operates in mammalian cells, Nat. Biotechnol., 25, 795, 10.1038/nbt1307
Ro, 2006, Production of the antimalarial drug precursor artemisinic acid in engineered yeast, Nature, 440, 940, 10.1038/nature04640
Rusconi, 2004, Antidote-mediated control of an anticoagulant aptamer in vivo, Nat. Biotechnol., 22, 1423, 10.1038/nbt1023
Rusconi, 2002, RNA aptamers as reversible antagonists of coagulation factor IXa, Nature, 419, 90, 10.1038/nature00963
Sakamoto, 1996, Intracellular cleavage of hepatitis C virus RNA and inhibition of viral protein translation by hammerhead ribozymes, J. Clin. Invest., 98, 2720, 10.1172/JCI119097
Seeman, 2005, From genes to machines: DNA nanomechanical devices, Trends Biochem. Sci., 30, 119, 10.1016/j.tibs.2005.01.007
Sharma, 2008, Engineering complex riboswitch regulation by dual genetic selection, J. Am. Chem. Soc., 130, 16310, 10.1021/ja805203w
Shetty, 2008, Engineering BioBrick vectors from BioBrick parts, J. Biol. Eng., 2, 5, 10.1186/1754-1611-2-5
Smolke, 2000, Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures, Appl. Environ. Microbiol., 66, 5399, 10.1128/AEM.66.12.5399-5405.2000
Smolke, 2001, Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization, Metab. Eng., 3, 313, 10.1006/mben.2001.0194
Soukup, 1999, Engineering precision RNA molecular switches, Proc. Natl. Acad. Sci. USA, 96, 3584, 10.1073/pnas.96.7.3584
Suess, 2004, A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo, Nucleic Acids Res., 32, 1610, 10.1093/nar/gkh321
Suess, 2003, Conditional gene expression by controlling translation with tetracycline-binding aptamers, Nucleic Acids Res., 31, 1853, 10.1093/nar/gkg285
Suess, 2008, Engineered riboswitches: overview, problems and trends, RNA Biol., 5, 24, 10.4161/rna.5.1.5955
Thompson, 2002, Group I aptazymes as genetic regulatory switches, BMC Biotechnol., 2, 21, 10.1186/1472-6750-2-21
Topp, 2007, Guiding bacteria with small molecules and RNA, J. Am. Chem. Soc., 129, 6807, 10.1021/ja0692480
Topp, 2008, Random walks to synthetic riboswitches–a high-throughput selection based on cell motility, ChemBioChem, 9, 210, 10.1002/cbic.200700546
Tuerk, 1990, Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, Science, 249, 505, 10.1126/science.2200121
Vaish, 1997, Isolation of hammerhead ribozymes with altered core sequences by in vitro selection, Biochemistry, 36, 6495, 10.1021/bi963134r
Vaish, 1998, Recent developments in the hammerhead ribozyme field, Nucleic Acids Res., 26, 5237, 10.1093/nar/26.23.5237
Waldminghaus, 2008, Generation of synthetic RNA-based thermosensors, Biol. Chem., 389, 1319, 10.1515/BC.2008.150
Wang, 2008, Splicing regulation: from a parts list of regulatory elements to an integrated splicing code, RNA, 14, 802, 10.1261/rna.876308
Wang, 2004, Systematic identification and analysis of exonic splicing silencers, Cell, 119, 831, 10.1016/j.cell.2004.11.010
Weigand, 2007, Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast, Nucleic Acids Res., 35, 4179, 10.1093/nar/gkm425
Werstuck, 1998, Controlling gene expression in living cells through small molecule-RNA interactions, Science, 282, 296, 10.1126/science.282.5387.296
Wieland, 2008, Improved aptazyme design and in vivo screening enable riboswitching in bacteria, Angew. Chem. Int. Ed. Engl., 47, 2604, 10.1002/anie.200703700
Win, 2007, From the Cover: A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, Proc. Natl. Acad. Sci. USA, 104, 14283, 10.1073/pnas.0703961104
Win, 2008, Higher-order cellular information processing with synthetic RNA devices, Science, 322, 456, 10.1126/science.1160311
Yen, 2004, Exogenous control of mammalian gene expression through modulation of RNA self-cleavage, Nature, 431, 471, 10.1038/nature02844
Yim, 2000, Translational suppression by hammerhead ribozymes and inactive variants in S. cerevisiae, Biomol. Eng., 16, 183, 10.1016/S1389-0344(99)00052-0
Yokobayashi, 2002, Directed evolution of a genetic circuit, Proc. Natl. Acad. Sci. USA, 99, 16587, 10.1073/pnas.252535999
Yoshimatsu, 1989, Control of gene expression by artificial introns in Saccharomyces cerevisiae, Science, 244, 1346, 10.1126/science.2544026
Zeng, 2002, Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells, Mol. Cell, 9, 1327, 10.1016/S1097-2765(02)00541-5
Zhou, 2003, Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae, Proc. Natl. Acad. Sci. USA, 100, 4457, 10.1073/pnas.0437993100
Zuker, 2003, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res., 31, 3406, 10.1093/nar/gkg595