Ligand-dependent ribozymes

Wiley Interdisciplinary Reviews: RNA

Volumn 8, Issue 2, 2017, Pages

  Felletti, Michele ^a   Hartig, Jörg S ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APTAZYME; GLMS RIBOZYME; LIGAND; OLIGONUCLEOTIDE; RIBONUCLEASE P; RIBOZYME; UNCLASSIFIED DRUG;

BACTERIAL GENE; BIOSENSOR; BIOTECHNOLOGY; EUKARYOTE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SWITCHING; GENE TECHNOLOGY; GENETIC ENGINEERING; HUMAN; IN VITRO STUDY; IN VIVO STUDY; LIGAND BINDING; NONHUMAN; PROTEIN RNA BINDING; REVIEW; RNA MOTIF; RNA STRUCTURE; ANIMAL; CONFORMATION; GENE THERAPY; GENETICS; METABOLISM; RNA SPLICING;

ANIMALS; GENETIC THERAPY; HUMANS; LIGANDS; NUCLEIC ACID CONFORMATION; RNA SPLICING; RNA, CATALYTIC;

EID: 84990064147     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1395     Document Type: Review

References (142)

1. Zaug AJ, Cech TR. In vitro splicing of the ribosomal RNA precursor in nuclei of Tetrahymena. Cell 1980, 19:331–338.
2. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983, 35:849–857.
3. Nielsen H, Johansen SD. Group I introns: moving in new directions. RNA Biol 2009, 6:375–383.
4. Esakova O, Krasilnikov AS. Of proteins and RNA: the RNase P/MRP family. RNA 2010, 16:1725–1747.
5. Lehmann K, Schmidt U. Group II introns: structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 2003, 38:249–303.
6. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science 2000, 289:920–930.
7. Jimenez RM, Polanco JA, Luptak A. Chemistry and biology of self-cleaving ribozymes. Trends Biochem Sci 2015, 40:648–661.
8. Prody GA, Bakos JT, Buzayan JM, Schneider IR, Bruening G. Autolytic processing of dimeric plant virus satellite RNA. Science 1986, 231:1577–1580.
9. Uhlenbeck OC. A small catalytic oligoribonucleotide. Nature 1987, 328:596–600.
10. Buzayan JM, Hampel A, Bruening G. Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res 1986, 14:9729–9743.
11. Sharmeen L, Kuo MY, Dinter-Gottlieb G, Taylor J. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 1988, 62:2674–2679.
12. Saville BJ, Collins RA. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 1990, 61:685–696.
13. Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004, 428:281–286.
14. Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol 2014, 10:56–60.
15. Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol 2015, 11:606–610.
16. Laha T, McManus DP, Loukas A, Brindley PJ. Sjα elements, short interspersed element-like retroposons bearing a hammerhead ribozyme motif from the genome of the oriental blood fluke Schistosoma japonicum. Biochim Biophys Acta 2000, 1492:477–482.
17. Ruminski DJ, Webb CH, Riccitelli NJ, Luptak A. Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes. J Biol Chem 2011, 286:41286–41295.
18. Garcia-Robles I, Sanchez-Navarro J, de la Pena M. Intronic hammerhead ribozymes in mRNA biogenesis. Biol Chem 2012, 393:1317–1326.
19. Collins JA, Irnov I, Baker S, Winkler WC. Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 2007, 21:3356–3368.
20. Fedor MJ, Williamson JR. The catalytic diversity of RNAs. Nat Rev Mol Cell Biol 2005, 6:399–412.
21. Robertson DL, Joyce GF. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 1990, 344:467–468.
22. Silverman SK. Artificial functional nucleic acids: aptamers, ribozymes and deoxyribozymes identified by in vitro selection. In: Li Y, Lu Y, eds. Functional Nucleic Acids for Analytical Applications. New York: Springer; 2009.
23. Frommer J, Appel B, Muller S. Ribozymes that can be regulated by external stimuli. Curr Opin Biotechnol 2015, 31:35–41.
24. Saragliadis A, Krajewski SS, Rehm C, Narberhaus F, Hartig JS. Thermozymes: synthetic RNA thermometers based on ribozyme activity. RNA Biol 2013, 10:1010–1016.
25. Keiper S, Vyle JS. Reversible photocontrol of deoxyribozyme-catalyzed RNA cleavage under multiple-turnover conditions. Angew Chem Int Ed Engl 2006, 45:3306–3309.
26. Nierth A, Singer M, Jaschke A. Efficient photoactivation of a Diels-Alderase ribozyme. Chem Commun (Camb) 2010, 46:7975–7977.
27. Breaker RR. Natural and engineered nucleic acids as tools to explore biology. Nature 2004, 432:838–845.
28. Golden BL. Two distinct catalytic strategies in the hepatitis delta virus ribozyme cleavage reaction. Biochemistry 2011, 50:9424–9433.
29. Brodersen DE, Nissen P. The social life of ribosomal proteins. FEBS J 2005, 272:2098–2108.
30. Kirsebom LA, Trobro S. RNase P RNA-mediated cleavage. IUBMB Life 2009, 61:189–200.
31. Smith JK, Hsieh J, Fierke CA. Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis. Biopolymers 2007, 87:329–338.
32. Evans D, Marquez SM, Pace NR. RNase P: interface of the RNA and protein worlds. Trends Biochem Sci 2006, 31:333–341.
33. Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N. A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription. Genes Dev 2006, 20:1621–1635.
34. Reiner R, Krasnov-Yoeli N, Dehtiar Y, Jarrous N. Function and assembly of a chromatin-associated RNase P that is required for efficient transcription by RNA polymerase I. PLoS One 2008, 3:e4072.
35. Pinker F, Bonnard G, Gobert A, Gutmann B, Hammani K, Sauter C, Gegenheimer PA, Giege P. PPR proteins shed a new light on RNase P biology. RNA Biol 2013, 10:1457–1468.
36. Cech TR, Zaug AJ, Grabowski PJ. In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 1981, 27:487–496.
37. Haugen P, Simon DM, Bhattacharya D. The natural history of group I introns. Trends Genet 2005, 21:111–119.
38. Solem A, Chatterjee P, Caprara MG. A novel mechanism for protein-assisted group I intron splicing. RNA 2002, 8:412–425.
39. Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 2010, 329:845–848.
40. Romling U, Galperin MY, Gomelsky M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 2013, 77:1–52.
41. McCown PJ, Roth A, Breaker RR. An expanded collection and refined consensus model of glmS ribozymes. RNA 2011, 17:728–736.
42. Cochrane JC, Lipchock SV, Strobel SA. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem Biol 2007, 14:97–105.
43. Breaker RR. Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 2012, 4:a003566.
44. Vicens Q, Westhof E. RNA as a drug target: the case of aminoglycosides. Chembiochem 2003, 4:1018–1023.
45. Hoch I, Berens C, Westhof E, Schroeder R. Antibiotic inhibition of RNA catalysis: neomycin B binds to the catalytic core of the td group I intron displacing essential metal ions. J Mol Biol 1998, 282:557–569.
46. Lambert T. Antibiotics that affect the ribosome. Rev Sci Tech 2012, 31:57–64.
47. Hermann T, Westhof E. Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J Mol Biol 1998, 276:903–912.
48. Jenne A, Hartig JS, Piganeau N, Tauer A, Samarsky DA, Green MR, Davies J, Famulok M. Rapid identification and characterization of hammerhead-ribozyme inhibitors using fluorescence-based technology. Nat Biotechnol 2001, 19:56–61.
49. Yen L, Svendsen J, Lee JS, Gray JT, Magnier M, Baba T, D'Amato RJ, Mulligan RC. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 2004, 431:471–476.
50. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 2010, 11:R31.
51. Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol 2011, 7:e1002031.
52. Porta H, Lizardi PM. An allosteric hammerhead ribozyme. Biotechnology 1995, 13:161–164.
53. Sargueil B, Pecchia DB, Burke JM. An improved version of the hairpin ribozyme functions as a ribonucleoprotein complex. Biochemistry 1995, 34:7739–7748.
54. Tang J, Breaker RR. Rational design of allosteric ribozymes. Chem Biol 1997, 4:453–459.
55. Hartig JS, Najafi-Shoushtari SH, Grune I, Yan A, Ellington AD, Famulok M. Protein-dependent ribozymes report molecular interactions in real time. Nat Biotechnol 2002, 20:717–722.
56. Beaudoin JD, Perreault JP. Potassium ions modulate a G-quadruplex-ribozyme's activity. RNA 2008, 14:1018–1025.
57. Amontov S, Jaschke A. Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes. Nucleic Acids Res 2006, 34:5032–5038.
58. Lam BJ, Joyce GF. Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA. Nat Biotechnol 2009, 27:288–292.
59. Robertson MP, Ellington AD. Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res 2000, 28:1751–1759.
60. Hall B, Hesselberth JR, Ellington AD. Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 2007, 22:1939–1947.
61. Penchovsky R. Computational design of allosteric ribozymes as molecular biosensors. Biotechnol Adv 2014, 32:1015–1027.
62. Soukup GA, Breaker RR. Engineering precision RNA molecular switches. Proc Natl Acad Sci USA 1999, 96:3584–3589.
63. Soukup GA, Emilsson GA, Breaker RR. Altering molecular recognition of RNA aptamers by allosteric selection. J Mol Biol 2000, 298:623–632.
64. Piganeau N, Jenne A, Thuillier V, Famulok M. An allosteric ribozyme regulated by doxycyline. Angew Chem Int Ed Engl 2000, 39:4369–4373.
65. Piganeau N, Thuillier V, Famulok M. In vitro selection of allosteric ribozymes: theory and experimental validation. J Mol Biol 2001, 312:1177–1190.
66. Strohbach D, Novak N, Muller S. Redox-active riboswitching: allosteric regulation of ribozyme activity by ligand-shape control. Angew Chem Int Ed Engl 2006, 45:2127–2129.
67. Jose AM, Soukup GA, Breaker RR. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 2001, 29:1631–1637.
68. Kertsburg A, Soukup GA. A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res 2002, 30:4599–4606.
69. Gu H, Furukawa K, Breaker RR. Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate. Anal Chem 2012, 84:4935–4941.
70. Najafi-Shoushtari SH, Famulok M. Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector. RNA 2005, 11:1514–1520.
71. Helm M, Petermeier M, Ge B, Fiammengo R, Jaschke A. Allosterically activated Diels-Alder catalysis by a ribozyme. J Am Chem Soc 2005, 127:10492–10493.
72. Lee HW, Robinson SG, Bandyopadhyay S, Mitchell RH, Sen D. Reversible photo-regulation of a hammerhead ribozyme using a diffusible effector. J Mol Biol 2007, 371:1163–1173.
73. Seetharaman S, Zivarts M, Sudarsan N, Breaker RR. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat Biotechnol 2001, 19:336–341.
74. Hesselberth JR, Robertson MP, Knudsen SM, Ellington AD. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal Biochem 2003, 312:106–112.
75. Knudsen SM, Lee J, Ellington AD, Savran CA. Ribozyme-mediated signal augmentation on a mass-sensitive biosensor. J Am Chem Soc 2006, 128:15936–15937.
76. Sun C, Liu X, Feng K, Jiang J, Shen G, Yu R. An aptazyme-based electrochemical biosensor for the detection of adenosine. Anal Chim Acta 2010, 669:87–93.
77. Ayukawa S, Sakai Y, Kiga D. An aptazyme-based molecular device that converts a small-molecule input into an RNA output. Chem Commun (Camb) 2012, 48:7556–7558.
78. Jenne A, Gmelin W, Raffler N, Famulok M. Real-time characterization of ribozymes by fluorescence resonance energy transfer (FRET). Angew Chem Int Ed Engl 1999, 38:1300–1303.
79. Vaish NK, Dong F, Andrews L, Schweppe RE, Ahn NG, Blatt L, Seiwert SD. Monitoring post-translational modification of proteins with allosteric ribozymes. Nat Biotechnol 2002, 20:810–815.
80. Srinivasan N, Kilburn JD. Combinatorial approaches to synthetic receptors. Curr Opin Chem Biol 2004, 8:305–310.
81. Sekella PT, Rueda D, Walter NG. A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage. RNA 2002, 8:1242–1252.
82. Hartig JS, Famulok M. Reporter ribozymes for real-time analysis of domain-specific interactions in biomolecules: HIV-1 reverse transcriptase and the primer-template complex. Angew Chem Int Ed Engl 2002, 41:4263–4266.
83. Ogawa A, Maeda M. Easy design of logic gates based on aptazymes and noncrosslinking gold nanoparticle aggregation. Chem Commun (Camb) 2009, (31):4666–4668.
84. Kuwabara T, Warashina M, Tanabe T, Tani K, Asano S, Taira K. A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo. Mol Cell 1998, 2:617–627.
85. Robertson MP, Ellington AD. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 1999, 17:62–66.
86. Vauleon S, Müller S. External regulation of hairpin ribozyme activity by an oligonucleotide effector. Chembiochem 2003, 4:220–224.
87. Burke DH, Ozerova ND, Nilsen-Hamilton M. Allosteric hammerhead ribozyme TRAPs. Biochemistry 2002, 41:6588–6594.
88. Najafi-Shoushtari SH, Mayer G, Famulok M. Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. Nucleic Acids Res 2004, 32:3212–3219.
89. Komatsu Y, Yamashita S, Kazama N, Nobuoka K, Ohtsuka E. Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor. J Mol Biol 2000, 299:1231–1243.
90. Wang DY, Lai BHY, Feldman AR, Sen D. A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. Nucleic Acids Res 2002, 30:1735–1742.
91. Wang DY, Lai BHY, Sen D. A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J Mol Biol 2002, 318:33–43.
92. Penchovsky R, Breaker RR. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol 2005, 23:1424–1433.
93. Bartel DP, Szostak JW. Isolation of new ribozymes from a large pool of random sequences. Science 1993, 261:1411–1418.
94. Komatsu Y, Nobuoka K, Karino-Abe N, Matsuda A, Ohtsuka E. In vitro selection of hairpin ribozymes activated with short oligonucleotides. Biochemistry 2002, 41:9090–9098.
95. Penchovsky R, Kostova GT. Computational selection and experimental validation of allosteric ribozymes that sense a specific sequence of human telomerase reverse transcriptase mRNAs as universal anticancer therapy agents. Nucleic Acid Ther 2013, 23:408–417.
96. Hartig JS, Grune I, Najafi-Shoushtari SH, Famulok M. Sequence-specific detection of microRNAs by signal-amplifying ribozymes. J Am Chem Soc 2004, 126:722–723.
97. Penchovsky R. Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics. ACS Synth Biol 2012, 1:471–482.
98. Wieland M, Fussenegger M. Engineering molecular circuits using synthetic biology in mammalian cells. Annu Rev Chem Biomol Eng 2012, 3:209–234.
99. Werstuck G, Green MR. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998, 282:296–298.
100. Thompson KM, Syrett HA, Knudsen SM, Ellington AD. Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2002, 2:21.
101. Win MN, Smolke CD. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci USA 2007, 104:14283–14288.
102. Wittmann A, Suess B. Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast. Mol Biosyst 2011, 7:2419–2427.
103. Link KH, Guo L, Ames TD, Yen L, Mulligan RC, Breaker RR. Engineering high-speed allosteric hammerhead ribozymes. Biol Chem 2007, 388:779–786.
104. Kato Y, Kuwabara T, Warashina M, Toda H, Taira K. Relationships between the activities in vitro and in vivo of various kinds of ribozyme and their intracellular localization in mammalian cells. J Biol Chem 2001, 276:15378–15385.
105. Carothers JM, Goler JA, Juminaga D, Keasling JD. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 2011, 334:1716–1719.
106. Wieland M, Hartig JS. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 2008, 47:2604–2607.
107. Nomura Y, Zhou L, Miu A, Yokobayashi Y. Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth Biol 2013, 2:684–689.
108. Auslander S, Ketzer P, Hartig JS. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol Biosyst 2010, 6:807–814.
109. Topp S, Gallivan JP. Random walks to synthetic riboswitches—a high-throughput selection based on cell motility. Chembiochem 2008, 9:210–213.
110. Nomura Y, Yokobayashi Y. Dual selection of a genetic switch by a single selection marker. Biosystems 2007, 90:115–120.
111. Lynch SA, Gallivan JP. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res 2009, 37:184–192.
112. Klauser B, Atanasov J, Siewert LK, Hartig JS. Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae. ACS Synth Biol 2015, 4:516–525.
113. Townshend B, Kennedy AB, Xiang JS, Smolke CD. High-throughput cellular RNA device engineering. Nat Methods 2015, 12:989–994.
114. Ogawa A, Maeda M. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 2007, 17:3156–3160.
115. Ogawa A, Maeda M. An artificial aptazyme-based riboswitch and its cascading system in E. coli. Chembiochem 2008, 9:206–209.
116. Wieland M, Gfell M, Hartig JS. Expanded hammerhead ribozymes containing addressable three-way junctions. RNA 2009, 15:968–976.
117. Wieland M, Benz A, Klauser B, Hartig JS. Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed Engl 2009, 48:2715–2718.
118. Feng X, Liu L, Duan X, Wang S. An engineered riboswitch as a potential gene-regulatory platform for reducing antibacterial drug resistance. Chem Commun (Camb) 2011, 47:173–175.
119. Smolke CD, Keasling JD. Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotechnol Bioeng 2002, 80:762–776.
120. Ogawa A, Maeda M. A novel label-free biosensor using an aptazyme-suppressor-tRNA conjugate and an amber mutated reporter gene. Chembiochem 2008, 9:2204–2208.
121. Berschneider B, Wieland M, Rubini M, Hartig JS. Small-molecule-dependent regulation of transfer RNA in bacteria. Angew Chem Int Ed Engl 2009, 48:7564–7567.
122. Saragliadis A, Hartig JS. Ribozyme-based transfer RNA switches for post-transcriptional control of amino acid identity in protein synthesis. J Am Chem Soc 2013, 135:8222–8226.
123. Klauser B, Saragliadis A, Auslander S, Wieland M, Berthold MR, Hartig JS. Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation. Mol Biosyst 2012, 8:2242–2248.
124. Wieland M, Berschneider B, Erlacher MD, Hartig JS. Aptazyme-mediated regulation of 16S ribosomal RNA. Chem Biol 2010, 17:236–242.
125. Wachter A. Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol 2010, 7:67–76.
126. Agop-Nersesian C, Pfahler J, Lanzer M, Meissner M. Functional expression of ribozymes in Apicomplexa: towards exogenous control of gene expression by inducible RNA-cleavage. Int J Parasitol 2008, 38:673–681.
127. Young DD, Garner RA, Yoder JA, Deiters A. Light-activation of gene function in mammalian cells via ribozymes. Chem Commun (Camb) 2009, 5:568–570.
128. Win MN, Smolke CD. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322:456–460.
129. Wieland M, Auslander D, Fussenegger M. Engineering of ribozyme-based riboswitches for mammalian cells. Methods 2012, 56:351–357.
130. Beilstein K, Wittmann A, Grez M, Suess B. Conditional control of mammalian gene expression by tetracycline-dependent hammerhead ribozymes. ACS Synth Biol 2015, 4:526–534.
131. Chen YY, Jensen MC, Smolke CD. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci USA 2010, 107:8531–8536.
132. Wei KY, Smolke CD. Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices. J Biol Eng 2015, 9:21.
133. Ketzer P, Kaufmann JK, Engelhardt S, Bossow S, von Kalle C, Hartig JS, Ungerechts G, Nettelbeck DM. Artificial riboswitches for gene expression and replication control of DNA and RNA viruses. Proc Natl Acad Sci USA 2014, 111:E554–E562.
134. Bell CL, Yu D, Smolke CD, Geall AJ, Beard CW, Mason PW. Control of αvirus-based gene expression using engineered riboswitches. Virology 2015, 483:302–311.
135. Scott WG, Horan LH, Martick M. The hammerhead ribozyme: structure, catalysis, and gene regulation. Prog Mol Biol Transl Sci 2013, 120:1–23.
136. Strobel B, Klauser B, Hartig JS, Lamla T, Gantner F, Kreuz S. Riboswitch-mediated attenuation of transgene cytotoxicity increases adeno-associated virus vector yields in HEK-293 cells. Mol Ther 2015, 23:1582–1591.
137. Kumar D, An CI, Yokobayashi Y. Conditional RNA interference mediated by allosteric ribozyme. J Am Chem Soc 2009, 131:13906–13907.
138. Bloom RJ, Winkler SM, Smolke CD. Synthetic feedback control using an RNAi-based gene-regulatory device. J Biol Eng 2015, 9:5.
139. Auslander S, Stucheli P, Rehm C, Auslander D, Hartig JS, Fussenegger M. A general design strategy for protein-responsive riboswitches in mammalian cells. Nat Methods 2014, 11:1154–1160.
140. Rouleau SG, Jodoin R, Bisaillon M, Perreault JP. Programming a highly structured ribozyme into complex allostery using RNA oligonucleotides. ACS Chem Biol 2012, 7:1802–1806.
141. Klauser B, Hartig JS. An engineered small RNA-mediated genetic switch based on a ribozyme expression platform. Nucleic Acids Res 2013, 41:5542–5552.
142. Matzner D, Mayer G. (Dis)similar analogues of riboswitch metabolites as antibacterial lead compounds. J Med Chem 2015, 58:3275–3286.