Zusammenfassung und Ausblick
7.4 Supplementary methods: Results and Discussion 3.3
7.4.9 Gene expression and quantification in E. coli
Experiments were performed using the Escherichia coli Top10 strain. All plasmids were transformed by electroporation. Bacterial cultures were cultivated in LB medium supplemented with 100 µg/mL carbenicillin. For eGFP expression measurement bacterial colonies were grown to stationary phase at 200 rpm and 37°C in an Infors HT Ecotron shaker. 100 µL of each culture were transferred into a 96-well microtiter plate and OD600 and the fluorescence of the expressed eGFP was measured with a Tecan Infinite® M200 plate reader (excitation wavelength: 488nm, emission wavelength 535 nm). Fluorescence values were corrected by dividing with the OD600 values. An equally treated culture which did not express any eGFP was used for subtraction of background fluorescence. All experiments were performed in triplicates and error bars represent standard deviations.
8. References
1. Khalil AS, Collins JJ. 2010. Synthetic biology: applications come of age. Nature reviews. Genetics 11:367-79
2. Chappell J, Takahashi MK, Meyer S, Loughrey D, Watters KE, Lucks J. 2013. The centrality of RNA for engineering gene expression. Biotechnology journal 8:1379-95 3. Vinkenborg JL, Karnowski N, Famulok M. 2011. Aptamers for allosteric regulation.
Nature chemical biology 7:519-27
4. Watson JD, Crick FH. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737-8
5. Saecker RM, Record MT, Jr., Dehaseth PL. 2011. Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. Journal of molecular biology 412:754-71
6. Borukhov S, Lee J, Laptenko O. 2005. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Molecular microbiology 55:1315-24 7. Peters JM, Vangeloff AD, Landick R. 2011. Bacterial transcription terminators: the
RNA 3'-end chronicles. Journal of molecular biology 412:793-813
8. Cruz JA, Westhof E. 2009. The dynamic landscapes of RNA architecture. Cell 136:604-9
9. Cech TR, Steitz JA. 2014. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157:77-94
10. Mignone F, Gissi C, Liuni S, Pesole G. 2002. Untranslated regions of mRNAs.
Genome biology 3:REVIEWS0004
11. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, et al. 2001.
Crystal structure of the ribosome at 5.5 A resolution. Science 292:883-96
12. Wilson DN, Doudna Cate JH. 2012. The structure and function of the eukaryotic ribosome. Cold Spring Harbor perspectives in biology 4
13. Giege R, Juhling F, Putz J, Stadler P, Sauter C, Florentz C. 2012. Structure of transfer RNAs: similarity and variability. Wiley interdisciplinary reviews. RNA 3:37-61 14. Shine J, Dalgarno L. 1974. The 3'-terminal sequence of Escherichia coli 16S
ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.
Proceedings of the National Academy of Sciences of the United States of America 71:1342-6
15. Kozak M. 1986. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283-92
16. Malys N, McCarthy JE. 2011. Translation initiation: variations in the mechanism can be anticipated. Cellular and molecular life sciences : CMLS 68:991-1003
17. Dunkle JA, Cate JH. 2010. Ribosome structure and dynamics during translocation and termination. Annual review of biophysics 39:227-44
18. Jacob F, Monod J. 1961. Genetic regulatory mechanisms in the synthesis of proteins.
Journal of molecular biology 3:318-56 causes RNA polymerase to pause during transcription in vitro. Nucleic acids research 9:563-77
22. Ciampi MS. 2006. Rho-dependent terminators and transcription termination.
Microbiology 152:2515-28
23. Proshkin S, Rahmouni AR, Mironov A, Nudler E. 2010. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328:504-8
24. Lee K, Holland-Staley CA, Cunningham PR. 1996. Genetic analysis of the Shine-Dalgarno interaction: selection of alternative functional mRNA-rRNA combinations.
Rna 2:1270-85
25. Hall MN, Gabay J, Debarbouille M, Schwartz M. 1982. A role for mRNA secondary structure in the control of translation initiation. Nature 295:616-8
26. Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, et al. 2008. Structure of eukaryotic RNA polymerases. Annual review of biophysics 37:337-52
27. Gallie DR. 1991. The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. Genes & development 5:2108-16
28. Banerjee AK. 1980. 5'-terminal cap structure in eucaryotic messenger ribonucleic acids. Microbiological reviews 44:175-205
29. McLauchlan J, Gaffney D, Whitton JL, Clements JB. 1985. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini. Nucleic acids research 13:1347-68
30. Lang WH, Morrow BE, Ju Q, Warner JR, Reeder RH. 1994. A model for transcription termination by RNA polymerase I. Cell 79:527-34
31. Hamada M, Sakulich AL, Koduru SB, Maraia RJ. 2000. Transcription termination by RNA polymerase III in fission yeast. A genetic and biochemically tractable model system. The Journal of biological chemistry 275:29076-81
32. Jackson RJ, Hellen CU, Pestova TV. 2010. The mechanism of eukaryotic translation initiation and principles of its regulation. Nature reviews. Molecular cell biology 11:113-27
36. Pabo CO, Sauer RT. 1992. Transcription factors: structural families and principles of DNA recognition. Annual review of biochemistry 61:1053-95
37. Estruch F. 2000. Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS microbiology reviews 24:469-86
38. Balleza E, Lopez-Bojorquez LN, Martinez-Antonio A, Resendis-Antonio O, Lozada-Chavez I, et al. 2009. Regulation by transcription factors in bacteria: beyond description. FEMS microbiology reviews 33:133-51
39. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic acids research 28:1838-47
40. Browning DF, Busby SJ. 2004. The regulation of bacterial transcription initiation.
Nature reviews. Microbiology 2:57-65
41. Lee DJ, Minchin SD, Busby SJ. 2012. Activating transcription in bacteria. Annual review of microbiology 66:125-52
42. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. 1982. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147-57
43. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-57
44. 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 391:806-11
45. Tomizawa J, Itoh T, Selzer G, Som T. 1981. Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA. Proceedings of the National Academy of Sciences of the United States of America 78:1421-5
46. Stougaard P, Molin S, Nordstrom K. 1981. RNAs involved in copy-number control and incompatibility of plasmid R1. Proceedings of the National Academy of Sciences of the United States of America 78:6008-12
47. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, et al. 2002. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111:747-56
48. Winkler WC, Cohen-Chalamish S, Breaker RR. 2002. An mRNA structure that controls gene expression by binding FMN. Proceedings of the National Academy of Sciences of the United States of America 99:15908-13
49. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-12 50. Waters LS, Storz G. 2009. Regulatory RNAs in bacteria. Cell 136:615-28
51. Kawamoto H, Koide Y, Morita T, Aiba H. 2006. Base-pairing requirement for RNA
54. Bandyra KJ, Said N, Pfeiffer V, Gorna MW, Vogel J, Luisi BF. 2012. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Molecular cell 47:943-53
55. Roth A, Breaker RR. 2009. The structural and functional diversity of metabolite-binding riboswitches. Annual review of biochemistry 78:305-34
56. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, et al. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
Science 306:275-9
57. Mandal M, Breaker RR. 2004. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature structural & molecular biology 11:29-35
58. Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, et al. 2012. Riboswitch control of Rho-dependent transcription termination. Proceedings of the National Academy of Sciences of the United States of America 109:5376-81
59. Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. 2008. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Molecular cell 29:691-702
60. Winkler W, Nahvi A, Breaker RR. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-6
61. Cheah MT, Wachter A, Sudarsan N, Breaker RR. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497-500
62. Caron MP, Bastet L, Lussier A, Simoneau-Roy M, Masse E, Lafontaine DA. 2012.
Dual-acting riboswitch control of translation initiation and mRNA decay. Proceedings of the National Academy of Sciences of the United States of America 109:E3444-53 63. Breaker RR. 2008. Complex riboswitches. Science 319:1795-7
64. Nou X, Kadner RJ. 2000. Adenosylcobalamin inhibits ribosome binding to btuB RNA.
Proceedings of the National Academy of Sciences of the United States of America 97:7190-5
65. Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, et al. 2006. Tandem riboswitch architectures exhibit complex gene control functions. Science 314:300-4 66. Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. 2004. Control of gene
expression by a natural metabolite-responsive ribozyme. Nature 428:281-6
67. Collins JA, Irnov I, Baker S, Winkler WC. 2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes & development 21:3356-68
68. Doudna JA, Cech TR. 2002. The chemical repertoire of natural ribozymes. Nature 418:222-8
69. Rupert PB, Ferre-D'Amare AR. 2001. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410:780-6
70. Ferre-D'Amare AR, Zhou K, Doudna JA. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395:567-74
71. Lafontaine DA, Norman DG, Lilley DM. 2002. The structure and active site of the
74. Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. 2014. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nature chemical biology 10:56-60
75. Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, et al. 2011. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations.
PLoS computational biology 7:e1002031
76. Chi YI, Martick M, Lares M, Kim R, Scott WG, Kim SH. 2008. Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS biology 6:e234
77. Hammann C, Luptak A, Perreault J, de la Pena M. 2012. The ubiquitous hammerhead ribozyme. Rna 18:871-85
78. Prody GA, Bakos JT, Buzayan JM, Schneider IR, Bruening G. 1986. Autolytic processing of dimeric plant virus satellite RNA. Science 231:1577-80
79. Jimenez RM, Delwart E, Luptak A. 2011. Structure-based search reveals hammerhead ribozymes in the human microbiome. The Journal of biological chemistry 286:7737-43
80. Seehafer C, Kalweit A, Steger G, Graf S, Hammann C. 2011. From alpaca to zebrafish: hammerhead ribozymes wherever you look. Rna 17:21-6
81. de la Pena M, Garcia-Robles I. 2010. Ubiquitous presence of the hammerhead ribozyme motif along the tree of life. Rna 16:1943-50
82. Hammann C, Lilley DM. 2002. Folding and activity of the hammerhead ribozyme.
Chembiochem : a European journal of chemical biology 3:690-700
83. Blount KF, Uhlenbeck OC. 2005. The structure-function dilemma of the hammerhead ribozyme. Annual review of biophysics and biomolecular structure 34:415-40
84. De la Pena M, Gago S, Flores R. 2003. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. The EMBO journal 22:5561-70 85. Forster AC, Symons RH. 1987. Self-cleavage of plus and minus RNAs of a virusoid
and a structural model for the active sites. Cell 49:211-20
86. Garcia-Robles I, Sanchez-Navarro J, de la Pena M. 2012. Intronic hammerhead ribozymes in mRNA biogenesis. Biological chemistry 393:1317-26
87. Win MN, Liang JC, Smolke CD. 2009. Frameworks for programming biological function through RNA parts and devices. Chemistry & biology 16:298-310
88. Ceres P, Trausch JJ, Batey RT. 2013. Engineering modular 'ON' RNA switches using biological components. Nucleic acids research
89. Wieland M, Benz A, Klauser B, Hartig JS. 2009. Artificial ribozyme switches containing natural riboswitch aptamer domains. Angewandte Chemie 48:2715-8 90. Garg A, Lohmueller JJ, Silver PA, Armel TZ. 2012. Engineering synthetic TAL
effectors with orthogonal target sites. Nucleic acids research 40:7584-95
91. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, et al. 2003. Expression profiling reveals off-target gene regulation by RNAi. Nature biotechnology 21:635-7 92. Acar M, Pando BF, Arnold FH, Elowitz MB, van Oudenaarden A. 2010. A general
mechanism for network-dosage compensation in gene circuits. Science 329:1656-60 93. Elowitz MB, Levine AJ, Siggia ED, Swain PS. 2002. Stochastic gene expression in a
single cell. Science 297:1183-6
94. Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. 2004.
Engineered riboregulators enable post-transcriptional control of gene expression.
Nature biotechnology 22:841-7
95. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. 2009. Synthetic gene networks that count. Science 324:1199-202
96. Callura JM, Cantor CR, Collins JJ. 2012. Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences of the United States of America 109:5850-5
97. Rodrigo G, Landrain TE, Jaramillo A. 2012. De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proceedings of the National Academy of Sciences of the United States of America 109:15271-6
98. Man S, Cheng R, Miao C, Gong Q, Gu Y, et al. 2011. Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria.
Nucleic acids research 39:e50
99. Sharma V, Yamamura A, Yokobayashi Y. 2012. Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS synthetic biology 1:6-13
100. Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. 2011. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proceedings of the National Academy of Sciences of the United States of America 108:8617-22
101. Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin AP. 2012. Rationally designed families of orthogonal RNA regulators of translation. Nature chemical biology 8:447-54
102. Ellington AD, Szostak JW. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-22
103. Tuerk C, Gold L. 1990. Systematic evolution of ligands by exponential enrichment:
RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-10
104. Werstuck G, Green MR. 1998. Controlling gene expression in living cells through small molecule-RNA interactions. Science 282:296-8
105. Suess B, Hanson S, Berens C, Fink B, Schroeder R, Hillen W. 2003. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic acids research 31:1853-8
106. Suess B, Fink B, Berens C, Stentz R, Hillen W. 2004. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic acids research 32:1610-4
107. Buskirk AR, Kehayova PD, Landrigan A, Liu DR. 2003. In vivo evolution of an RNA-based transcriptional activator. Chemistry & biology 10:533-40
108. Buskirk AR, Landrigan A, Liu DR. 2004. Engineering a ligand-dependent RNA transcriptional activator. Chemistry & biology 11:1157-63
109. Wachsmuth M, Findeiss S, Weissheimer N, Stadler PF, Morl M. 2013. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic acids research 41:2541-51
110. Ceres P, Garst AD, Marcano-Velazquez JG, Batey RT. 2013. Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS synthetic biology 2:463-72
111. Ceres P, Trausch JJ, Batey RT. 2013. Engineering modular 'ON' RNA switches using biological components. Nucleic acids research 41:10449-61
112. Kim DS, Gusti V, Pillai SG, Gaur RK. 2005. An artificial riboswitch for controlling pre-mRNA splicing. Rna 11:1667-77
113. Weigand JE, Suess B. 2007. Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic acids research 35:4179-85
114. Culler SJ, Hoff KG, Smolke CD. 2010. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330:1251-5
115. Thompson KM, Syrett HA, Knudsen SM, Ellington AD. 2002. Group I aptazymes as genetic regulatory switches. BMC biotechnology 2:21
116. Balke D, Wichert C, Appel B, Muller S. 2014. Generation and selection of ribozyme variants with potential application in protein engineering and synthetic biology.
Applied microbiology and biotechnology 98:3389-99
117. Khvorova A, Lescoute A, Westhof E, Jayasena SD. 2003. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nature structural biology 10:708-12
118. Yen L, Svendsen J, Lee JS, Gray JT, Magnier M, et al. 2004. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431:471-6
119. Yen L, Magnier M, Weissleder R, Stockwell BR, Mulligan RC. 2006. Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries. Rna 12:797-806
120. Jenne A, Hartig JS, Piganeau N, Tauer A, Samarsky DA, et al. 2001. Rapid identification and characterization of hammerhead-ribozyme inhibitors using fluorescence-based technology. Nature biotechnology 19:56-61
121. Tang J, Breaker RR. 1997. Rational design of allosteric ribozymes. Chemistry &
biology 4:453-9
122. Win MN, Smolke CD. 2007. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proceedings of the National Academy of Sciences of the United States of America 104:14283-8
123. Liang JC, Chang AL, Kennedy AB, Smolke CD. 2012. A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity. Nucleic acids research 40:e154
124. Win MN, Smolke CD. 2008. Higher-order cellular information processing with synthetic RNA devices. Science 322:456-60
125. Wieland M, Hartig JS. 2008. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angewandte Chemie 47:2604-7
126. Deana A, Celesnik H, Belasco JG. 2008. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature 451:355-8
127. Auslander S, Ketzer P, Hartig JS. 2010. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Molecular bioSystems 6:807-14 128. Ketzer P, Haas SF, Engelhardt S, Hartig JS, Nettelbeck DM. 2012. Synthetic
riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses. Nucleic acids research 40:e167
129. Ketzer P, Kaufmann JK, Engelhardt S, Bossow S, von Kalle C, et al. 2014. Artificial riboswitches for gene expression and replication control of DNA and RNA viruses.
Proceedings of the National Academy of Sciences of the United States of America 111:E554-62
130. Berschneider B, Wieland M, Rubini M, Hartig JS. 2009. Small-molecule-dependent regulation of transfer RNA in bacteria. Angewandte Chemie 48:7564-7
131. Wieland M, Berschneider B, Erlacher MD, Hartig JS. 2010. Aptazyme-mediated regulation of 16S ribosomal RNA. Chemistry & biology 17:236-42
132. Kumar D, An CI, Yokobayashi Y. 2009. Conditional RNA interference mediated by allosteric ribozyme. Journal of the American Chemical Society 131:13906-7
133. Saragliadis A, Hartig JS. 2013. Ribozyme-based transfer RNA switches for post-transcriptional control of amino acid identity in protein synthesis. Journal of the American Chemical Society 135:8222-6
134. Lynch SA, Desai SK, Sajja HK, Gallivan JP. 2007. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chemistry &
biology 14:173-84
135. Lynch SA, Gallivan JP. 2009. A flow cytometry-based screen for synthetic riboswitches. Nucleic acids research 37:184-92
136. Nomura Y, Yokobayashi Y. 2007. Reengineering a natural riboswitch by dual genetic selection. Journal of the American Chemical Society 129:13814-5
137. Topp S, Gallivan JP. 2007. Guiding bacteria with small molecules and RNA. Journal of the American Chemical Society 129:6807-11
138. Weigand JE, Sanchez M, Gunnesch EB, Zeiher S, Schroeder R, Suess B. 2008.
Screening for engineered neomycin riboswitches that control translation initiation.
Rna 14:89-97
139. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic acids research 31:3406-15
140. Saragliadis A, Krajewski SS, Rehm C, Narberhaus F, Hartig JS. 2013. Thermozymes:
Synthetic RNA thermometers based on ribozyme activity. RNA biology 10:1010-6 141. Storz G, Vogel J, Wassarman KM. 2011. Regulation by small RNAs in bacteria:
expanding frontiers. Molecular cell 43:880-91
142. Penchovsky R, Breaker RR. 2005. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature biotechnology 23:1424-33 143. Burke DH, Ozerova ND, Nilsen-Hamilton M. 2002. Allosteric hammerhead ribozyme
TRAPs. Biochemistry 41:6588-94
144. Komatsu Y, Yamashita S, Kazama N, Nobuoka K, Ohtsuka E. 2000. Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor. Journal of molecular biology 299:1231-43
145. Ferbeyre G, Smith JM, Cedergren R. 1998. Schistosome satellite DNA encodes active hammerhead ribozymes. Molecular and cellular biology 18:3880-8
146. Levine E, Zhang Z, Kuhlman T, Hwa T. 2007. Quantitative characteristics of gene regulation by small RNA. PLoS biology 5:e229
147. Levine E, Hwa T. 2008. Small RNAs establish gene expression thresholds. Current opinion in microbiology 11:574-9
148. Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ. 2010. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences of the United States of America 107:15898-903
149. Franch T, Petersen M, Wagner EG, Jacobsen JP, Gerdes K. 1999. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. Journal of molecular biology 294:1115-25
150. Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL, 3rd, Al-Hashimi HM. 2012.
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic acids research 40:1345-55
151. Carothers JM, Goler JA, Juminaga D, Keasling JD. 2011. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 334:1716-9 152. Mitarai N, Benjamin JA, Krishna S, Semsey S, Csiszovszki Z, et al. 2009. Dynamic
features of gene expression control by small regulatory RNAs. Proceedings of the National Academy of Sciences of the United States of America 106:10655-9
153. Papenfort K, Podkaminski D, Hinton JC, Vogel J. 2012. The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proceedings of the National Academy of Sciences of the United States of America 109:E757-64
154. Sharma V, Yamamura A, Yokobayashi Y. 2012. Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli. Acs Synth Biol 1:6-13
155. Urban JH, Vogel J. 2007. Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic acids research 35:1018-37
156. Dixon N, Duncan JN, Geerlings T, Dunstan MS, McCarthy JE, et al. 2010.
Reengineering orthogonally selective riboswitches. Proceedings of the National Academy of Sciences of the United States of America 107:2830-5
157. Delebecque CJ, Lindner AB, Silver PA, Aldaye FA. 2011. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333:470-4
158. Berschneider B, Wieland M, Rubini M, Hartig JS. 2009. Small-Molecule-Dependent Regulation of Transfer RNA in Bacteria. Angew Chem Int Edit 48:7564-7
159. Wieland M, Berschneider B, Erlacher MD, Hartig JS. 2010. Aptazyme-Mediated Regulation of 16S Ribosomal RNA. Chem Biol 17:236-42
160. Wieland M, Fussenegger M. 2012. Reprogrammed cell delivery for personalized medicine. Advanced drug delivery reviews 64:1477-87
161. Stynen B, Tournu H, Tavernier J, Van Dijck P. 2012. Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiology and molecular biology reviews : MMBR 76:331-82
162. Ringner M, Krogh M. 2005. Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS computational biology
162. Ringner M, Krogh M. 2005. Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS computational biology