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Engineering RNA-Based Circuits

  • R. Narayanaswamy
  • A.D. Ellington
Part of the Handbook of Experimental Pharmacology book series (HEP, volume 173)

Abstract

Nucleic acids can modulate gene function by base-pairing, via the molecular recognition of proteins and metabolites, and by catalysis. This diversity of functions can be combined with the ability to engineer nucleic acids based on Watson-Crick base-pairing rules to create a modular set of molecular “tools” for biotechnological and medical interventions in cellular metabolism. However, these individual RNA-based tools are most powerful when combined into rational logical or regulatory circuits, and the circuits can in turn be evolved for optimal function. Examples of genetic circuits that control translation and transcription are herein detailed, and more complex circuits with medical applications are anticipated.

Keywords

siRNA (small interfering RNA) miRNA (microRNA) RNAi (RNA interference) UTR (untranslated region) RBS (ribosome binding site) 

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References

  1. Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024PubMedGoogle Scholar
  2. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207PubMedGoogle Scholar
  3. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF (2004) The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 11:816–821CrossRefPubMedGoogle Scholar
  4. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427:839–843CrossRefPubMedGoogle Scholar
  5. Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355CrossRefPubMedGoogle Scholar
  6. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11:941–950CrossRefPubMedGoogle Scholar
  7. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5:101–113PubMedGoogle Scholar
  8. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefPubMedGoogle Scholar
  9. Bartel DP, Chen CZ (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5:396–400CrossRefPubMedGoogle Scholar
  10. Batey RT, Gilbert SD, Montange RK (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432:411–415CrossRefPubMedGoogle Scholar
  11. Baugh C, Grate D, Wilson C (2000) 2.8 Å crystal structure of the malachite green aptamer. J Mol Biol 301:117–128CrossRefPubMedGoogle Scholar
  12. Bayer TS, Smolke CD (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 23:337–343CrossRefPubMedGoogle Scholar
  13. Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) Anautonomous molecular computer for logical control of gene expression. Nature 429:423–429CrossRefPubMedGoogle Scholar
  14. Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428:431–437CrossRefPubMedGoogle Scholar
  15. Blake WJ, M KA, Cantor CR, Collins JJ (2003) Noise in eukaryotic gene expression. Nature 422:633–637CrossRefPubMedGoogle Scholar
  16. Blount KF, Uhlenbeck OC (2005) The structure-function dilemma of the hammerhead ribozyme. Annu Rev Biophys Biomol Struct 34:415–440CrossRefPubMedGoogle Scholar
  17. Brantl S (2004) Bacterial gene regulation: from transcription attenuation to riboswitches and ribozymes. Trends Microbiol 12:473–475CrossRefPubMedGoogle Scholar
  18. Breaker RR (2004) Natural and engineered nucleic acids as tools to explore biology. Nature 432:838–845CrossRefPubMedGoogle Scholar
  19. Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Biol 1:223–229CrossRefPubMedGoogle Scholar
  20. Brescia CC, Mikulecky PJ, Feig AL, Sledjeski DD (2003) Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA 9:33–43CrossRefPubMedGoogle Scholar
  21. Buskirk AR, Landrigan A, Liu DR (2004a) Engineering a ligand-dependent RNA transcriptional activator. Chem Biol 11:1157–1163CrossRefPubMedGoogle Scholar
  22. Buskirk AR, Ong YC, Gartner ZJ, Liu DR (2004b) Directed evolution of ligand dependence: small-molecule-activated protein splicing. Proc Natl Acad Sci U S A 101:10505–10510CrossRefPubMedGoogle Scholar
  23. Byun J, Lan N, Long M, Sullenger BA(2003) Efficient and specific repair of sickle beta-globin RNA by trans-splicing ribozymes. RNA 9:1254–1263CrossRefPubMedGoogle Scholar
  24. Carpousis AJ (2002) The Escherichia coli RNA degradosome: structure, function and relationship in other ribonucleolytic multienzyme complexes. Biochem Soc Trans 30:150–155PubMedGoogle Scholar
  25. Carter RJ, Dubchak I, Holbrook SR (2001) A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res 29:3928–3938PubMedGoogle Scholar
  26. Cech TR, Zaug AJ, Grabowski PJ (1981) In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27:487–496CrossRefPubMedGoogle Scholar
  27. Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB (2002) A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65:157–177PubMedGoogle Scholar
  28. Chen S, Zhang A, Blyn LB, Storz G (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186:6689–6697PubMedGoogle Scholar
  29. Citti L, Rainaldi G (2005) Synthetic hammerhead ribozymes as therapeutic tools to control disease genes. Curr Gene Ther 5:11–24PubMedGoogle Scholar
  30. Cox JC, Cohen DS, Ellington AD (1999) The complexities of DNA computation. Trends Biotechnol 17:151–154CrossRefPubMedGoogle Scholar
  31. Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD (2002) Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 30:e108CrossRefPubMedGoogle Scholar
  32. Crooke ST (2004) Progress in antisense technology. Annu Rev Med 55:61–95CrossRefPubMedGoogle Scholar
  33. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686CrossRefPubMedGoogle Scholar
  34. Doudna JA, Cech TR (2002) The chemical repertoire of natural ribozymes. Nature 418:222–228CrossRefPubMedGoogle Scholar
  35. Dykxhoorn DM, Lieberman J (2005) The silent revolution: RNA interference asbasic biology, research tool, and therapeutic. Annu Rev Med 56:401–423CrossRefPubMedGoogle Scholar
  36. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338CrossRefPubMedGoogle Scholar
  37. Emilsson GM, Breaker RR (2002) Deoxyribozymes: new activities and new applications. Cell Mol Life Sci 59:596–607PubMedGoogle Scholar
  38. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA (2004) B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 11:822–829CrossRefPubMedGoogle Scholar
  39. Famulok M, Mayer G (1999) Aptamers as tools in molecular biology and immunology. Curr Top Microbiol Immunol 243:123–136PubMedGoogle Scholar
  40. Fan P, Suri AK, Fiala R, Live D, Patel DJ (1996) Molecular recognition in the FMN-RNA aptamer complex. J Mol Biol 258:480–500CrossRefPubMedGoogle Scholar
  41. Ferre-D’Amare AR, Zhou K, Doudna JA (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395:567–574PubMedGoogle Scholar
  42. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811CrossRefPubMedGoogle Scholar
  43. Fraser AG, Marcotte EM (2004) A probabilistic view of gene function. Nat Genet 36:559–564CrossRefPubMedGoogle Scholar
  44. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O’shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737–741CrossRefPubMedGoogle Scholar
  45. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391CrossRefPubMedGoogle Scholar
  46. Gottesman S (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58:303–328CrossRefPubMedGoogle Scholar
  47. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121–D124PubMedGoogle Scholar
  48. Hesselberth J, Robertson MP, Jhaveri S, Ellington AD (2000) In vitro selection of nucleic acids for diagnostic applications. J Biotechnol 74:15–25PubMedGoogle Scholar
  49. Hesselberth JR, Robertson MP, Knudsen SM, Ellington AD (2003) Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal Biochem 312:106–112CrossRefPubMedGoogle Scholar
  50. Howard K (2003) Unlocking the money-making potential of RNAi. Nat Biotechnol 21:1441–1446PubMedGoogle Scholar
  51. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O’shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425:686–691CrossRefPubMedGoogle Scholar
  52. Huppi K, Martin SE, Caplen NJ (2005) Defining and assaying RNAi in mammalian cells. Mol Cell 17:1–10CrossRefPubMedGoogle Scholar
  53. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297:2056–2060CrossRefPubMedGoogle Scholar
  54. Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22:841–847CrossRefPubMedGoogle Scholar
  55. Iyo M, Kawasaki H, Taira K (2002) Construction of an allosteric trans-maxizyme targeting for two distinct oncogenes. Nucleic Acids Res Suppl 115–116Google Scholar
  56. Iyo M, Kawasaki H, Taira K (2004) Maxizyme technology. Methods Mol Biol 252:257–265PubMedGoogle Scholar
  57. Jayasena SD (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45:1628–1650PubMedGoogle Scholar
  58. Jenison RD, Gill SC, Pardi A, Polisky B (1994) High-resolution molecular discrimination by RNA. Science 263:1425–1429PubMedGoogle Scholar
  59. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ (2005) RAS is regulated by the let-7 microRNA family. Cell 120:635–647CrossRefPubMedGoogle Scholar
  60. Jose AM, Soukup GA, Breaker RR (2001) Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 29:1631–1637CrossRefPubMedGoogle Scholar
  61. Joshi P, Prasad VR (2002) Potent inhibition of human immunodeficiency virus type 1 replication by template analog reverse transcriptase inhibitors derived by SELEX (systematic evolution of ligands by exponential enrichment). J Virol 76:6545–6557CrossRefPubMedGoogle Scholar
  62. Kaern M, Blake WJ, Collins JJ (2003) The engineering of gene regulatory networks. Annu Rev Biomed Eng 5:179–206CrossRefPubMedGoogle Scholar
  63. Karberg M, Guo H, Zhong J, Coon R, Perutka J, Lambowitz AM (2001) Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nat Biotechnol 19:1162–1167CrossRefPubMedGoogle Scholar
  64. Kertsburg A, Soukup GA (2002) A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res 30:4599–4606CrossRefPubMedGoogle Scholar
  65. Khan AU, Lal SK (2003) Ribozymes: a modern tool in medicine. J Biomed Sci 10:457–467PubMedGoogle Scholar
  66. Koizumi M, Soukup GA, Kerr JN, Breaker RR (1999) Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat Struct Biol 6:1062–1071PubMedGoogle Scholar
  67. Komatsu Y, Yamashita S, Kazama N, Nobuoka K, Ohtsuka E (2000) Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor. J Mol Biol 299:1231–1243CrossRefPubMedGoogle Scholar
  68. Kore AR, Vaish NK, Kutzke U, Eckstein F (1998) Sequence specificity of the hammerhead ribozyme revisited; the NHH rule. Nucleic Acids Res 26:4116–4120CrossRefPubMedGoogle Scholar
  69. Kuwabara T, Warashina M, Tanabe T, Tani K, Asano S, Taira K (1998) A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo. Mol Cell 2:617–627CrossRefPubMedGoogle Scholar
  70. Lambowitz AM, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35CrossRefPubMedGoogle Scholar
  71. Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, Tsai MJ, O’Malley BW (1999) A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97:17–27CrossRefPubMedGoogle Scholar
  72. Lanz RB, Razani B, Goldberg AD, O’Malley BW (2002) Distinct RNA motifs are important for coactivation of steroid hormone receptors by steroid receptor RNA activator (SRA). Proc Natl Acad Sci U S A 99:16081–16086CrossRefPubMedGoogle Scholar
  73. Lazarev D, Puskarz I, Breaker RR (2003) Substrate specificity and reaction kinetics of an X-motif ribozyme. RNA 9:688–697CrossRefPubMedGoogle Scholar
  74. Lee I, Date SV, Adai AT, Marcotte EM (2004) A probabilistic functional network of yeast genes. Science 306:1555–1558PubMedGoogle Scholar
  75. Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118:69–82CrossRefPubMedGoogle Scholar
  76. Mackie GA, Genereaux JL (1993) The role of RNA structure in determining RNase E-dependent cleavage sites in the mRNA for ribosomal protein S20 in vitro. J Mol Biol 234:998–1012CrossRefPubMedGoogle Scholar
  77. Mandal M, Breaker RR (2004a) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 11:29–35CrossRefPubMedGoogle Scholar
  78. Mandal M, Breaker RR (2004b) Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5:451–463CrossRefPubMedGoogle Scholar
  79. Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113:577–586CrossRefPubMedGoogle Scholar
  80. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR (2004) Aglycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306:275–279CrossRefPubMedGoogle Scholar
  81. Mansfield SG, Chao H, Walsh CE (2004) RNA repair using spliceosome-mediated RNA trans-splicing. Trends Mol Med 10:263–268CrossRefPubMedGoogle Scholar
  82. Marshall KA, Ellington AD (2000) In vitro selection of RNA aptamers. Methods Enzymol 318:193–214PubMedGoogle Scholar
  83. Masse E, Gottesman S (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99:4620–4625CrossRefPubMedGoogle Scholar
  84. Masse E, Majdalani N, Gottesman S (2003) Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol 6:120–124PubMedGoogle Scholar
  85. Matzke MA, Birchler JA (2005) RNAi-mediated pathways in the nucleus. Nat Rev Genet 6:24–35CrossRefPubMedGoogle Scholar
  86. McDowall KJ, Lin-Chao S, Cohen SN (1994) A+Ucontent rather than a particular nucleotide order determines the specificity of RNase E cleavage. J Biol Chem 269:10790–10796PubMedGoogle Scholar
  87. Michienzi A, Castanotto D, Lee N, Li S, Zaia JA, Rossi JJ (2003) RNA-mediated inhibition of HIV in a gene therapy setting. Ann N Y Acad Sci 1002:63–71CrossRefPubMedGoogle Scholar
  88. Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL (2004) Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat Struct Mol Biol 11:1206–1214CrossRefPubMedGoogle Scholar
  89. Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U (2003) Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9:1308–1314CrossRefPubMedGoogle Scholar
  90. Moore PB, Steitz TA (2003) The structural basis of large ribosomal subunit function. Annu Rev Biochem 72:813–850CrossRefPubMedGoogle Scholar
  91. Nimjee SM, Rusconi CP, Sullenger BA (2005) Aptamers: an emerging class of therapeutics. Annu Rev Med 56:555–583CrossRefPubMedGoogle Scholar
  92. Opdyke JA, Kang JG, Storz G (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186:6698–6705CrossRefPubMedGoogle Scholar
  93. Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O’shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428:427–431CrossRefPubMedGoogle Scholar
  94. Pan WH, Xin P, Bui V, Clawson GA (2003) Rapid identification of efficient target cleavage sites using a hammerhead ribozyme library in an iterative manner. Mol Ther 7:129–139CrossRefPubMedGoogle Scholar
  95. Parker JS, Roe SM, Barford D (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434:663–666CrossRefPubMedGoogle Scholar
  96. Perutka J, Wang W, Goerlitz D, Lambowitz AM (2004) Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genes. J Mol Biol 336:421–439CrossRefPubMedGoogle Scholar
  97. Pley HW, Flaherty KM, McKay DB (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372:68–74PubMedGoogle Scholar
  98. Pollack JR, Iyer VR (2002) Characterizing the physical genome. Nat Genet 32Suppl 515–521PubMedGoogle Scholar
  99. Puerta-Fernandez E, Romero-Lopez C, Barroso-delJesus A, Berzal-Herranz A (2003) Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 27:75–97PubMedGoogle Scholar
  100. Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold R (2003) The study of macromolecular complexes by quantitative proteomics. Nat Genet 33:349–355CrossRefPubMedGoogle Scholar
  101. Raser JM, O’shea EK (2004) Control of stochasticity in eukaryotic gene expression. Science 304:1811–1814CrossRefPubMedGoogle Scholar
  102. Rivas E, Klein RJ, Jones TA, Eddy SR (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:1369–1373CrossRefPubMedGoogle Scholar
  103. Robertson MP, Ellington AD (1999) In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 17:62–66PubMedGoogle Scholar
  104. Robertson MP, Ellington AD (2000) Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res 28:1751–1759PubMedGoogle Scholar
  105. Robertson MP, Knudsen SM, Ellington AD (2004) In vitro selection of ribozymes dependent on peptides for activity. RNA 10:114–127CrossRefPubMedGoogle Scholar
  106. Roth A, Breaker RR (2004) Selection in vitro of allosteric ribozymes. Methods Mol Biol 252:145–164PubMedGoogle Scholar
  107. Rupert PB, Ferre-D’Amare AR (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410:780–786CrossRefPubMedGoogle Scholar
  108. Rusconi CP, Scardino E, Layzer J, Pitoc GA, Ortel TL, Monroe D, Sullenger BA (2002) RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419:90–94CrossRefPubMedGoogle Scholar
  109. Santoro SW, Joyce GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci U S A 94:4262–4266PubMedGoogle Scholar
  110. Seydoux G, Mello CC, Pettitt J, Wood WB, Priess JR, Fire A (1996) Repression of gene expression in the embryonic germ lineage of C. elegans. Nature 382:713–716CrossRefPubMedGoogle Scholar
  111. Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ (2004) RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci U S A 101:6548–6552CrossRefPubMedGoogle Scholar
  112. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434:462–469PubMedGoogle Scholar
  113. Sontheimer EJ (2005) Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 6:127–138CrossRefPubMedGoogle Scholar
  114. Soukup GA, Breaker RR (2000) Allosteric nucleic acid catalysts. Curr Opin Struct Biol 10:318–325CrossRefPubMedGoogle Scholar
  115. Steitz TA, Moore PB (2003) RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci 28:411–418CrossRefPubMedGoogle Scholar
  116. Stojanovic MN, Stefanovic D (2003) A deoxyribozyme-based molecular automaton. Nat Biotechnol 21:1069–1074CrossRefPubMedGoogle Scholar
  117. Storz, Wassarman KM (2004) An abundance of RNA regulators. Annu Rev Biochem 74:199–217Google Scholar
  118. Storz G, Opdyke JA, Zhang A (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7:140–144CrossRefPubMedGoogle Scholar
  119. Sudarsan N, Barrick JE, Breaker RR (2003)Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9:644–647CrossRefPubMedGoogle Scholar
  120. Sullenger BA, Gilboa E (2002) Emerging clinical applications of RNA. Nature 418:252–258CrossRefPubMedGoogle Scholar
  121. Suyama E, Kawasaki H, Wadhwa R, Taira K (2004a) Cell migration and metastasis as targets of small RNA-based molecular genetic analyses. J Muscle Res Cell Motil 25:303–308CrossRefPubMedGoogle Scholar
  122. Suyama E, Wadhwa R, Kaur K, Miyagishi M, Kaul SC, Kawasaki H, Taira K (2004b) Identification of metastasis-related genes in a mouse model using a library of randomized ribozymes. J Biol Chem 279:38083–38086CrossRefPubMedGoogle Scholar
  123. Tang G, Zamore PD (2004) Biochemical dissection of RNA silencing in plants. Methods Mol Biol 257:223–244PubMedGoogle Scholar
  124. Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17:49–63CrossRefPubMedGoogle Scholar
  125. Tang J, Breaker RR (1997) Rational design of allosteric ribozymes. Chem Biol 4:453–459CrossRefPubMedGoogle Scholar
  126. Tang J, Breaker RR (2000) Structural diversity of self-cleaving ribozymes. Proc Natl Acad Sci U S A 97:5784–5789PubMedGoogle Scholar
  127. Thompson KM, Syrett HA, Knudsen SM, Ellington AD (2002) Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2:21CrossRefPubMedGoogle Scholar
  128. Tomari Y, Zamore PD (2005) Perspective: machines for RNAi. Genes Dev 19:517–529CrossRefPubMedGoogle Scholar
  129. Vaish NK, Dong F, Andrews L, Schweppe RE, Ahn NG, Blatt L, Seiwert SD (2002) Monitoring post-translational modification of proteins with allosteric ribozymes. Nat Biotechnol 20:810–815PubMedGoogle Scholar
  130. Vaish NK, Kossen K, Andrews LE, Pasko C, Seiwert SD (2004) Monitoring protein modification with allosteric ribozymes. Methods 32:428–436CrossRefPubMedGoogle Scholar
  131. Vytvytska O, Moll I, Kaberdin VR, von Gabain A, Blasi U (2000) Hfq (HF1) stimulates ompA mRNA decay by interfering with ribosome binding. Genes Dev 14:1109–1118PubMedGoogle Scholar
  132. Wadhwa R, Yaguchi T, Kaur K, Suyama E, Kawasaki H, Taira K, Kaul SC (2004) Use of a randomized hybrid ribozyme library for identification of genes involved in muscle differentiation. J Biol Chem 279:51622–51629CrossRefPubMedGoogle Scholar
  133. Wassarman KM, Storz G (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell 101:613–623CrossRefPubMedGoogle Scholar
  134. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637–1651CrossRefPubMedGoogle Scholar
  135. Wilderman PJ, Sowa NA, FitzGerald DJ, FitzGerald PC, Gottesman S, Ochsner UA, Vasil ML (2004) Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc Natl Acad Sci U S A 101:9792–9797CrossRefPubMedGoogle Scholar
  136. Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611–647CrossRefPubMedGoogle Scholar
  137. Winkler WC, Cohen-Chalamish S, Breaker RR (2002) An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci U S A 99:15908–15913PubMedGoogle Scholar
  138. Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428:281–286CrossRefPubMedGoogle Scholar
  139. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594–596CrossRefPubMedGoogle Scholar
  140. Yen L, Svendsen J, Lee JS, Gray JT, Magnier M, Baba T, D’Amato RJ, Mulligan RC (2004) Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431:471–476CrossRefPubMedGoogle Scholar
  141. Yokobayashi Y, Weiss R, Arnold FH (2002) Directed evolution of a genetic circuit. Proc Natl Acad Sci U S A 99:16587–16591CrossRefPubMedGoogle Scholar
  142. Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:1111–1124PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • R. Narayanaswamy
    • 1
  • A.D. Ellington
    • 1
  1. 1.Institute for Cellular and Molecular BiologyUniversity of TexasAustinUSA

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