-
1
-
-
84897128298
-
The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones
-
Cech, T.R.; Steitz, J.A. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones. Cell 2014, 157, 77–94.
-
(2014)
Cell
, vol.157
, pp. 77-94
-
-
Cech, T.R.1
Steitz, J.A.2
-
2
-
-
84874706897
-
Riboswitches: A Common RNA Regulatory Element
-
Edwards, A.L.; Batey, R.T. Riboswitches: A Common RNA Regulatory Element. Nat. Educ. 2010, 3, 9.
-
(2010)
Nat. Educ
, vol.3
, pp. 9
-
-
Edwards, A.L.1
Batey, R.T.2
-
3
-
-
85011941305
-
Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs
-
Narberhaus, F. Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs. RNA Biol. 2010, 7, 84–89.
-
(2010)
RNA Biol
, vol.7
, pp. 84-89
-
-
Narberhaus, F.1
-
4
-
-
72749118512
-
A pH-responsive riboregulator
-
Nechooshtan, G.; Elgrably-Weiss, M.; Sheaffer, A.; Westhof, E.; Altuvia, S. A pH-responsive riboregulator. Genes Dev. 2009, 23, 2650–2662.
-
(2009)
Genes Dev
, vol.23
, pp. 2650-2662
-
-
Nechooshtan, G.1
Elgrably-Weiss, M.2
Sheaffer, A.3
Westhof, E.4
Altuvia, S.5
-
5
-
-
0025074907
-
In vitro selection of RNA molecules that bind specific ligands
-
Ellington, A.D.; Szostak, J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818–822.
-
(1990)
Nature
, vol.346
, pp. 818-822
-
-
Ellington, A.D.1
Szostak, J.W.2
-
6
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505–510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
7
-
-
70349769485
-
Chemical synthesis using synthetic biology
-
Carothers, J.M.; Goler, J.A.; Keasling, J.D. Chemical synthesis using synthetic biology. Curr. Opin. Biotechnol. 2009, 20, 498–503.
-
(2009)
Curr. Opin. Biotechnol
, vol.20
, pp. 498-503
-
-
Carothers, J.M.1
Goler, J.A.2
Keasling, J.D.3
-
8
-
-
84961653881
-
Emerging applications of riboswitches—From antibacterial targets to molecular tools
-
Machtel, P.; Bąkowska-Żywicka, K.; Żywicki, M. Emerging applications of riboswitches—From antibacterial targets to molecular tools. J. Appl. Genet. 2016, 57, 531–541.
-
(2016)
J. Appl. Genet
, vol.57
, pp. 531-541
-
-
Machtel, P.1
Bąkowska-Żywicka, K.2
Żywicki, M.3
-
9
-
-
80052975908
-
Engineering biological systems with synthetic RNA molecules
-
Liang, J.C.; Bloom, R.J.; Smolke, C.D. Engineering biological systems with synthetic RNA molecules. Mol. Cell 2011, 43, 915–926.
-
(2011)
Mol. Cell
, vol.43
, pp. 915-926
-
-
Liang, J.C.1
Bloom, R.J.2
Smolke, C.D.3
-
10
-
-
84948415786
-
Synthetic biology devices for in vitro and in vivo diagnostics
-
Slomovic, S.; Pardee, K.; Collins, J.J. Synthetic biology devices for in vitro and in vivo diagnostics. Proc. Natl. Acad. Sci. USA 2015, 112, 14429–14435.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 14429-14435
-
-
Slomovic, S.1
Pardee, K.2
Collins, J.J.3
-
11
-
-
2542601538
-
A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo
-
Suess, B.; Fink, B.; Berens, C.; Stentz, R.; Hillen, W. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res. 2004, 32, 1610–1614.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1610-1614
-
-
Suess, B.1
Fink, B.2
Berens, C.3
Stentz, R.4
Hillen, W.5
-
12
-
-
84906052564
-
Riboswitch engineering—Making the all-important second and third steps
-
Berens, C.; Suess, B. Riboswitch engineering—Making the all-important second and third steps. Curr. Opin. Biotechnol. 2015, 31, 10–15.
-
(2015)
Curr. Opin. Biotechnol.
, vol.31
, pp. 10-15
-
-
Berens, C.1
Suess, B.2
-
13
-
-
84934985382
-
A renaissance in RNA synthetic biology: New mechanisms, applications and tools for the future
-
Chappell, J.; Watters, K.E.; Takahashi, M.K.; Lucks, J.B. A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future. Curr. Opin. Chem. Biol. 2015, 28, 47–56.
-
(2015)
Curr. Opin. Chem. Biol
, vol.28
, pp. 47-56
-
-
Chappell, J.1
Watters, K.E.2
Takahashi, M.K.3
Lucks, J.B.4
-
14
-
-
84965158377
-
Opportunities in the design and application of RNA for gene expression control
-
McKeague, M.; Wong, R.S.; Smolke, C.D. Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res. 2016, 44, 2987–2999.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. 2987-2999
-
-
McKeague, M.1
Wong, R.S.2
Smolke, C.D.3
-
15
-
-
85014820996
-
Synthetic Riboswitches: From Plug and Pray toward Plug and Play
-
Etzel, M.; Mörl, M. Synthetic Riboswitches: From Plug and Pray toward Plug and Play. Biochemistry 2017, 56, 1181–1198.
-
(2017)
Biochemistry
, vol.56
, pp. 1181-1198
-
-
Etzel, M.1
Mörl, M.2
-
16
-
-
0036753365
-
Genetic control by a metabolite binding mRNA
-
Nahvi, A.; Sudarsan, N.; Ebert, M.S.; Zou, X.; Brown, K.L.; Breaker, R.R. Genetic control by a metabolite binding mRNA. Chem. Biol. 2002, 9, 1043–1049.
-
(2002)
Chem. Biol
, vol.9
, pp. 1043-1049
-
-
Nahvi, A.1
Sudarsan, N.2
Ebert, M.S.3
Zou, X.4
Brown, K.L.5
Breaker, R.R.6
-
17
-
-
18744396047
-
Sensing small molecules by nascent RNA: A mechanism to control transcription in bacteria
-
Mironov, A.S.; Gusarov, I.; Rafikov, R.; Lopez, L.E.; Shatalin, K.; Kreneva, R.A.; Perumov, D.A.; Nudler, E. Sensing small molecules by nascent RNA: A mechanism to control transcription in bacteria. Cell 2002, 111, 747–756.
-
(2002)
Cell
, vol.111
, pp. 747-756
-
-
Mironov, A.S.1
Gusarov, I.2
Rafikov, R.3
Lopez, L.E.4
Shatalin, K.5
Kreneva, R.A.6
Perumov, D.A.7
Nudler, E.8
-
18
-
-
0028224199
-
High-resolution molecular discrimination by RNA
-
Jenison, R.D.; Gill, S.C.; Pardi, A.; Polisky, B. High-resolution molecular discrimination by RNA. Science 1994, 263, 1425–1429.
-
(1994)
Science
, vol.263
, pp. 1425-1429
-
-
Jenison, R.D.1
Gill, S.C.2
Pardi, A.3
Polisky, B.4
-
19
-
-
0037432340
-
Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex
-
Jucker, F.M.; Phillips, R.M.; McCallum, S.A.; Pardi, A. Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex. Biochemistry 2003, 42, 2560–2567.
-
(2003)
Biochemistry
, vol.42
, pp. 2560-2567
-
-
Jucker, F.M.1
Phillips, R.M.2
McCallum, S.A.3
Pardi, A.4
-
20
-
-
0036235684
-
Inhibition of translation by RNA-small molecule interactions
-
Harvey, I.; Garneau, P.; Pelletier, J. Inhibition of translation by RNA-small molecule interactions. RNA 2002, 8, 452–463.
-
(2002)
RNA
, vol.8
, pp. 452-463
-
-
Harvey, I.1
Garneau, P.2
Pelletier, J.3
-
21
-
-
6044261460
-
Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation
-
Desai, S.K.; Gallivan, J.P. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc. 2004, 126, 13247–13254.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 13247-13254
-
-
Desai, S.K.1
Gallivan, J.P.2
-
22
-
-
54349119816
-
A FACS-based approach to engineering artificial riboswitches
-
Fowler, C.C.; Brown, E.D.; Li, Y. A FACS-based approach to engineering artificial riboswitches. Chembiochem 2008, 9, 1906–1911.
-
(2008)
Chembiochem
, vol.9
, pp. 1906-1911
-
-
Fowler, C.C.1
Brown, E.D.2
Li, Y.3
-
23
-
-
84876376374
-
De novo design of a synthetic riboswitch that regulates transcription termination
-
Wachsmuth, M.; Findeiß, S.; Weissheimer, N.; Stadler, P.F.; Mörl, M. de novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res. 2013, 41, 2541–2551.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 2541-2551
-
-
Wachsmuth, M.1
Findeiß, S.2
Weissheimer, N.3
Stadler, P.F.4
Mörl, M.5
-
24
-
-
77950423140
-
Ultrafast Dynamics Show That the Theophylline and 3-Methylxanthine Aptamers Employ a Conformational Capture Mechanism for Binding Their Ligands
-
Lee, S.W.; Zhao, L.; Pardi, A.; Xia, T. Ultrafast Dynamics Show That the Theophylline and 3-Methylxanthine Aptamers Employ a Conformational Capture Mechanism for Binding Their Ligands. Biochemistry 2010, 49, 2943–2951.
-
(2010)
Biochemistry
, vol.49
, pp. 2943-2951
-
-
Lee, S.W.1
Zhao, L.2
Pardi, A.3
Xia, T.4
-
25
-
-
0030752211
-
Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
-
Zimmermann, G.R.; Jenison, R.D.; Wick, C.L.; Simorre, J.P.; Pardi, A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat. Struct. Biol. 1997, 4, 644–649.
-
(1997)
Nat. Struct. Biol
, vol.4
, pp. 644-649
-
-
Zimmermann, G.R.1
Jenison, R.D.2
Wick, C.L.3
Simorre, J.P.4
Pardi, A.5
-
26
-
-
78650475424
-
Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR
-
Wunnicke, D.; Strohbach, D.; Weigand, J.E.; Appel, B.; Feresin, E.; Suess, B.; Müller, S.; Steinhoff, H.J. Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR. RNA 2011, 17, 182–188.
-
(2011)
RNA
, vol.17
, pp. 182-188
-
-
Wunnicke, D.1
Strohbach, D.2
Weigand, J.E.3
Appel, B.4
Feresin, E.5
Suess, B.6
Müller, S.7
Steinhoff, H.J.8
-
27
-
-
0034853943
-
A tetracycline-binding RNA aptamer
-
Berens, C.; Thain, A.; Schroeder, R. A tetracycline-binding RNA aptamer. Bioorg. Med. Chem. 2001, 9, 2549–2556.
-
(2001)
Bioorg. Med. Chem
, vol.9
, pp. 2549-2556
-
-
Berens, C.1
Thain, A.2
Schroeder, R.3
-
28
-
-
15444379109
-
Molecular analysis of a synthetic tetracycline-binding riboswitch
-
Hanson, S.; Bauer, G.; Fink, B.; Suess, B. Molecular analysis of a synthetic tetracycline-binding riboswitch. RNA 2005, 11, 503–511.
-
(2005)
RNA
, vol.11
, pp. 503-511
-
-
Hanson, S.1
Bauer, G.2
Fink, B.3
Suess, B.4
-
29
-
-
0037388001
-
Conditional gene expression by controlling translation with tetracycline-binding aptamers
-
Suess, B.; Hanson, S.; Berens, C.; Fink, B.; Schroeder, R.; Hillen, W. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res. 2003, 31, 1853–1858.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 1853-1858
-
-
Suess, B.1
Hanson, S.2
Berens, C.3
Fink, B.4
Schroeder, R.5
Hillen, W.6
-
30
-
-
34547639506
-
Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast
-
Weigand, J.E.; Suess, B. Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic Acids Res. 2007, 35, 4179–4185.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4179-4185
-
-
Weigand, J.E.1
Suess, B.2
-
31
-
-
53649104514
-
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch
-
Xiao, H.; Edwards, T.E.; Ferré-D’Amaré, A.R. Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem. Biol. 2008, 15, 1125–1137.
-
(2008)
Chem. Biol
, vol.15
, pp. 1125-1137
-
-
Xiao, H.1
Edwards, T.E.2
Ferré-D’amaré, A.R.3
-
32
-
-
84857851763
-
Conformational dynamics of the tetracycline-binding aptamer
-
Forster, U.; Weigand, J.E.; Trojanowski, P.; Suess, B.; Wachtveitl, J. Conformational dynamics of the tetracycline-binding aptamer. Nucleic Acids Res. 2012, 40, 1807–1817.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 1807-1817
-
-
Forster, U.1
Weigand, J.E.2
Trojanowski, P.3
Suess, B.4
Wachtveitl, J.5
-
33
-
-
0141677751
-
Tetracycline-aptamer-mediated translational regulation in yeast
-
Hanson, S.; Berthelot, K.; Fink, B.; McCarthy, J.E.G.; Suess, B. Tetracycline-aptamer-mediated translational regulation in yeast. Mol. Microbiol. 2003, 49, 1627–1637.
-
(2003)
Mol. Microbiol
, vol.49
, pp. 1627-1637
-
-
Hanson, S.1
Berthelot, K.2
Fink, B.3
McCarthy, J.E.G.4
Suess, B.5
-
34
-
-
33646909444
-
Thermodynamic characterization of an engineered tetracycline-binding riboswitch
-
Müller, M.; Weigand, J.E.; Weichenrieder, O.; Suess, B. Thermodynamic characterization of an engineered tetracycline-binding riboswitch. Nucleic Acids Res. 2006, 34, 2607–2617.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2607-2617
-
-
Müller, M.1
Weigand, J.E.2
Weichenrieder, O.3
Suess, B.4
-
35
-
-
84863617223
-
Engineered riboswitches: Expanding researcher’s toolbox with synthetic RNA regulators
-
Wittmann, A.; Suess, B. Engineered riboswitches: Expanding researcher’s toolbox with synthetic RNA regulators. FEBS Lett. 2012, 586, 2076–2083.
-
(2012)
FEBS Lett
, vol.586
, pp. 2076-2083
-
-
Wittmann, A.1
Suess, B.2
-
37
-
-
38049004429
-
Screening for engineered neomycin riboswitches that control translation initiation
-
Weigand, J.E.; Sanchez, M.; Gunnesch, E.B.; Zeiher, S.; Schroeder, R.; Suess, B. Screening for engineered neomycin riboswitches that control translation initiation. RNA 2008, 14, 89–97.
-
(2008)
RNA
, vol.14
, pp. 89-97
-
-
Weigand, J.E.1
Sanchez, M.2
Gunnesch, E.B.3
Zeiher, S.4
Schroeder, R.5
Suess, B.6
-
38
-
-
79955613663
-
Mechanistic insights into an engineered riboswitch: A switching element which confers riboswitch activity
-
Weigand, J.E.; Schmidtke, S.R.; Will, T.J.; Duchardt-Ferner, E.; Hammann, C.; Wöhnert, J.; Suess, B. Mechanistic insights into an engineered riboswitch: A switching element which confers riboswitch activity. Nucleic Acids Res. 2011, 39, 3363–3372.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 3363-3372
-
-
Weigand, J.E.1
Schmidtke, S.R.2
Will, T.J.3
Duchardt-Ferner, E.4
Hammann, C.5
Wöhnert, J.6
Suess, B.7
-
39
-
-
84956744124
-
What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch
-
Duchardt-Ferner, E.; Gottstein-Schmidtke, S.R.; Weigand, J.E.; Ohlenschlager, O.; Wurm, J.P.; Hammann, C.; Suess, B.; Wöhnert, J. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew. Chem. 2016, 55, 1527–1530.
-
(2016)
Angew. Chem
, vol.55
, pp. 1527-1530
-
-
Duchardt-Ferner, E.1
Gottstein-Schmidtke, S.R.2
Weigand, J.E.3
Ohlenschlager, O.4
Wurm, J.P.5
Hammann, C.6
Suess, B.7
Wöhnert, J.8
-
40
-
-
77649260489
-
Reengineering orthogonally selective riboswitches
-
Dixon, N.; Duncan, J.N.; Geerlings, T.; Dunstan, M.S.; McCarthy, J.E.G.; Leys, D.; Micklefield, J. Reengineering orthogonally selective riboswitches. Proc. Natl. Acad. Sci. USA 2010, 107, 2830–2835.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 2830-2835
-
-
Dixon, N.1
Duncan, J.N.2
Geerlings, T.3
Dunstan, M.S.4
McCarthy, J.E.G.5
Leys, D.6
Micklefield, J.7
-
41
-
-
84937683269
-
Rational Re-engineering of a Transcriptional Silencing PreQ1Riboswitch
-
Wu, M.C.; Lowe, P.T.; Robinson, C.J.; Vincent, H.A.; Dixon, N.; Leigh, J.; Micklefield, J. Rational Re-engineering of a Transcriptional Silencing PreQ1Riboswitch. J. Am. Chem. Soc. 2015, 137, 9015–9021.
-
(2015)
J. Am. Chem. Soc
, vol.137
, pp. 9015-9021
-
-
Wu, M.C.1
Lowe, P.T.2
Robinson, C.J.3
Vincent, H.A.4
Dixon, N.5
Leigh, J.6
Micklefield, J.7
-
42
-
-
14644393547
-
Green fluorescent protein is a quantitative reporter of gene expression in individual eukaryotic cells
-
Soboleski, M.R.; Oaks, J.; Halford, W.P. Green fluorescent protein is a quantitative reporter of gene expression in individual eukaryotic cells. FASEB J. 2005, 19, 440–442.
-
(2005)
FASEB J
, vol.19
, pp. 440-442
-
-
Soboleski, M.R.1
Oaks, J.2
Halford, W.P.3
-
43
-
-
0003785155
-
-
Cold Spring Habor Laboratory Press: Cold Spring Habor, NY, USA
-
Miller, J.H. (Ed.) Experiments in Molecular Genetics; Cold Spring Habor Laboratory Press: Cold Spring Habor, NY, USA, 1972.
-
(1972)
Experiments in Molecular Genetics
-
-
Miller, J.H.1
-
44
-
-
33847039871
-
A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function
-
Lynch, S.A.; Desai, S.K.; Sajja, H.K.; Gallivan, J.P. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem. Biol. 2007, 14, 173–184.
-
(2007)
Chem. Biol
, vol.14
, pp. 173-184
-
-
Lynch, S.A.1
Desai, S.K.2
Sajja, H.K.3
Gallivan, J.P.4
-
45
-
-
0030249526
-
Direct Selection of Tetracycline-Sensitive Escherichia coli Cells Using Nickel Salts
-
Podolsky, T.; Fong, S.T.; Lee, B.T.O. Direct Selection of Tetracycline-Sensitive Escherichia coli Cells Using Nickel Salts. Plasmid 1996, 36, 112–115.
-
(1996)
Plasmid
, vol.36
, pp. 112-115
-
-
Podolsky, T.1
Fong, S.T.2
Lee, B.T.O.3
-
46
-
-
0034284280
-
Expression of the tetA(C) tetracycline efflux pump in Escherichia coli confers osmotic sensitivity
-
Stavropoulos, T.A.; Strathdee, C.A. Expression of the tetA(C) tetracycline efflux pump in Escherichia coli confers osmotic sensitivity. FEMS Microbiol. Lett. 2000, 190, 147–150.
-
(2000)
FEMS Microbiol. Lett
, vol.190
, pp. 147-150
-
-
Stavropoulos, T.A.1
Strathdee, C.A.2
-
47
-
-
70350523604
-
Mechanism-guided library design and dual genetic selection of synthetic OFF riboswitches
-
Muranaka, N.; Abe, K.; Yokobayashi, Y. Mechanism-guided library design and dual genetic selection of synthetic OFF riboswitches. Chembiochem 2009, 10, 2375–2381.
-
(2009)
Chembiochem
, vol.10
, pp. 2375-2381
-
-
Muranaka, N.1
Abe, K.2
Yokobayashi, Y.3
-
48
-
-
63249090231
-
An efficient platform for genetic selection and screening of gene switches in Escherichia coli
-
Muranaka, N.; Sharma, V.; Nomura, Y.; Yokobayashi, Y. An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Res. 2009, 37, e39.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Muranaka, N.1
Sharma, V.2
Nomura, Y.3
Yokobayashi, Y.4
-
49
-
-
34249806305
-
Guiding bacteria with small molecules and RNA
-
Topp, S.; Gallivan, J.P. Guiding bacteria with small molecules and RNA. J. Am. Chem. Soc. 2007, 129, 6807–6811.
-
(2007)
J. Am. Chem. Soc
, vol.129
, pp. 6807-6811
-
-
Topp, S.1
Gallivan, J.P.2
-
50
-
-
0034460297
-
How signals are heard during bacterial chemotaxis: Protein-protein interactions in sensory signal propagation
-
Bren, A.; Eisenbach, M. How signals are heard during bacterial chemotaxis: Protein-protein interactions in sensory signal propagation. J. Bacteriol. 2000, 182, 6865–6873.
-
(2000)
J. Bacteriol
, vol.182
, pp. 6865-6873
-
-
Bren, A.1
Eisenbach, M.2
-
51
-
-
38849129508
-
Random walks to synthetic riboswitches-a high-throughput selection based on cell motility
-
Topp, S.; Gallivan, J.P. Random walks to synthetic riboswitches-a high-throughput selection based on cell motility. Chembiochem 2008, 9, 210–213.
-
(2008)
Chembiochem
, vol.9
, pp. 210-213
-
-
Topp, S.1
Gallivan, J.P.2
-
52
-
-
0026509195
-
A uridine-rich sequence required for translation of prokaryotic mRNA
-
Zhang, J.; Deutscher, M.P. A uridine-rich sequence required for translation of prokaryotic mRNA. Proc. Natl. Acad. Sci. USA 1992, 89, 2605–2609.
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 2605-2609
-
-
Zhang, J.1
Deutscher, M.P.2
-
53
-
-
79960959180
-
RNA Mimics of Green Fluorescent Protein
-
Paige, J.S.; Wu, K.Y.; Jaffrey, S.R. RNA Mimics of Green Fluorescent Protein. Science 2011, 333, 637–642.
-
(2011)
Science
, vol.333
, pp. 637-642
-
-
Paige, J.S.1
Wu, K.Y.2
Jaffrey, S.R.3
-
54
-
-
84963815342
-
Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells
-
Litke, J.L.; You, M.; Jaffrey, S.R. Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells. Meth. Enzymol. 2016, 572, 315–333.
-
(2016)
Meth. Enzymol
, vol.572
, pp. 315-333
-
-
Litke, J.L.1
You, M.2
Jaffrey, S.R.3
-
55
-
-
84930227077
-
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch
-
You, M.; Litke, J.L.; Jaffrey, S.R. Imaging metabolite dynamics in living cells using a Spinach-based riboswitch. Proc. Natl. Acad. Sci. USA 2015, 112, 2756–2765.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 2756-2765
-
-
You, M.1
Litke, J.L.2
Jaffrey, S.R.3
-
56
-
-
84979257985
-
Engineering and characterization of fluorogenic glycine riboswitches
-
Ketterer, S.; Gladis, L.; Kozica, A.; Meier, M. Engineering and characterization of fluorogenic glycine riboswitches. Nucleic Acids Res. 2016, 44, 5983–5992.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. 5983-5992
-
-
Ketterer, S.1
Gladis, L.2
Kozica, A.3
Meier, M.4
-
57
-
-
84875784381
-
RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messengers Cyclic di-GMP and Cyclic AMP-GMP
-
Kellenberger, C.A.; Wilson, S.C.; Sales-Lee, J.; Hammond, M.C. RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messengers Cyclic di-GMP and Cyclic AMP-GMP. J. Am. Chem. Soc. 2013, 135, 4906–4909.
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 4906-4909
-
-
Kellenberger, C.A.1
Wilson, S.C.2
Sales-Lee, J.3
Hammond, M.C.4
-
58
-
-
84858030373
-
Fluorescence Imaging of Cellular Metabolites with RNA
-
Paige, J.S.; Nguyen-Duc, T.; Song, W.; Jaffrey, S.R. Fluorescence Imaging of Cellular Metabolites with RNA. Science 2012, 335, 1194.
-
(2012)
Science
, vol.335
, pp. 1194
-
-
Paige, J.S.1
Nguyen-Duc, T.2
Song, W.3
Jaffrey, S.R.4
-
59
-
-
84913570361
-
Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution
-
Filonov, G.S.; Moon, J.D.; Svensen, N.; Jaffrey, S.R. Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 2014, 136, 16299–16308.
-
(2014)
J. Am. Chem. Soc
, vol.136
, pp. 16299-16308
-
-
Filonov, G.S.1
Moon, J.D.2
Svensen, N.3
Jaffrey, S.R.4
-
60
-
-
84908193573
-
RNA mango aptamer-fluorophore: A bright, high-affinity complex for RNA labeling and tracking. ACS
-
Dolgosheina, E.V.; Jeng, S.C.Y.; Panchapakesan, S.S.S.; Cojocaru, R.; Chen, P.S.K.; Wilson, P.D.; Hawkins, N.; Wiggins, P.A.; Unrau, P.J. RNA mango aptamer-fluorophore: A bright, high-affinity complex for RNA labeling and tracking. ACS Chem. Biol. 2014, 9, 2412–2420.
-
(2014)
Chem. Biol
, vol.9
, pp. 2412-2420
-
-
Dolgosheina, E.V.1
Jeng, S.C.Y.2
Panchapakesan, S.S.S.3
Cojocaru, R.4
Chen, P.S.K.5
Wilson, P.D.6
Hawkins, N.7
Wiggins, P.A.8
Unrau, P.J.9
-
61
-
-
84889649107
-
Contact-Mediated Quenching for RNA Imaging in Bacteria with a Fluorophore-Binding Aptamer
-
Sunbul, M.; Jäschke, A. Contact-Mediated Quenching for RNA Imaging in Bacteria with a Fluorophore-Binding Aptamer. Angew. Chem. Int. Ed. 2013, 52, 13401–13404.
-
Angew. Chem. Int. Ed. 2013
, vol.52
, pp. 13401-13404
-
-
Sunbul, M.1
Jäschke, A.2
-
62
-
-
84983770697
-
Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers
-
Arora, A.; Sunbul, M.; Jäschke, A. Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers. Nucleic Acids Res. 2015, 43, doi:10.1093/nar/gkv718.
-
(2015)
Nucleic Acids Res
, vol.43
-
-
Arora, A.1
Sunbul, M.2
Jäschke, A.3
-
63
-
-
84948471468
-
Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells
-
Zhang, J.; Fei, J.; Leslie, B.J.; Han, K.Y.; Kuhlman, T.E.; Ha, T. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci. Rep. 2015, 5, 17295.
-
(2015)
Sci. Rep
, vol.5
, pp. 17295
-
-
Zhang, J.1
Fei, J.2
Leslie, B.J.3
Han, K.Y.4
Kuhlman, T.E.5
Ha, T.6
-
64
-
-
0348133608
-
RNA sensors: Novel regulators of gene expression
-
Kaempfer, R. RNA sensors: Novel regulators of gene expression. EMBO Rep. 2003, 4, 1043–1047.
-
(2003)
EMBO Rep
, vol.4
, pp. 1043-1047
-
-
Kaempfer, R.1
-
65
-
-
0033120034
-
The Mechanism of Intrinsic Transcription Termination
-
Gusarov, I.; Nudler, E. The Mechanism of Intrinsic Transcription Termination. Mol. Cell 1999, 3, 495–504.
-
(1999)
Mol. Cell
, vol.3
, pp. 495-504
-
-
Gusarov, I.1
Nudler, E.2
-
66
-
-
79954597274
-
Termination and antitermination: RNA polymerase runs a stop sign
-
Santangelo, T.J.; Artsimovitch, I. Termination and antitermination: RNA polymerase runs a stop sign. Nat. Rev. Microbiol. 2011, 9, 319–329.
-
(2011)
Nat. Rev. Microbiol
, vol.9
, pp. 319-329
-
-
Santangelo, T.J.1
Artsimovitch, I.2
-
67
-
-
55449129670
-
Prediction of transcriptional terminators in Bacillus subtilis and related species
-
De Hoon, M.J.L.; Makita, Y.; Nakai, K.; Miyano, S. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput. Biol. 2005, 1, e25.
-
(2005)
Plos Comput. Biol
, vol.1
-
-
De Hoon, M.J.L.1
Makita, Y.2
Nakai, K.3
Miyano, S.4
-
68
-
-
0019331859
-
DNA-RNA hybrid duplexes containing oligo(DA:rU) sequences are exceptionally unstable and may facilitate termination of transcription
-
Martin, F.H.; Tinoco, I. DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 1980, 8, 2295–2300.
-
(1980)
Nucleic Acids Res
, vol.8
, pp. 2295-2300
-
-
Martin, F.H.1
Tinoco, I.2
-
69
-
-
84928267620
-
Design criteria for synthetic riboswitches acting on transcription
-
Wachsmuth, M.; Domin, G.; Lorenz, R.; Serfling, R.; Findeiß, S.; Stadler, P.F.; Mörl, M. Design criteria for synthetic riboswitches acting on transcription. RNA Biol. 2015, 12, 221–231.
-
(2015)
RNA Biol
, vol.12
, pp. 221-231
-
-
Wachsmuth, M.1
Domin, G.2
Lorenz, R.3
Serfling, R.4
Findeiß, S.5
Stadler, P.F.6
Mörl, M.7
-
70
-
-
79960395328
-
Bacterial Transcription Terminators: The RNA 3’-End Chronicles
-
Peters, J.M.; Vangeloff, A.D.; Landick, R. Bacterial Transcription Terminators: The RNA 3’-End Chronicles. J. Mol. Biol. 2011, 412, 793–813.
-
(2011)
J. Mol. Biol
, vol.412
, pp. 793-813
-
-
Peters, J.M.1
Vangeloff, A.D.2
Landick, R.3
-
71
-
-
68349141373
-
RNA synthetic biology inspired from bacteria: Construction of transcription attenuators under antisense regulation
-
Dawid, A.; Cayrol, B.; Isambert, H. RNA synthetic biology inspired from bacteria: Construction of transcription attenuators under antisense regulation. Phys. Biol. 2009, 6, 25007.
-
(2009)
Phys. Biol
, vol.6
, pp. 25007
-
-
Dawid, A.1
Cayrol, B.2
Isambert, H.3
-
72
-
-
84863226500
-
Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals
-
Qi, L.; Lucks, J.B.; Liu, C.C.; Mutalik, V.K.; Arkin, A.P. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012, 40, 5775–5786.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5775-5786
-
-
Qi, L.1
Lucks, J.B.2
Liu, C.C.3
Mutalik, V.K.4
Arkin, A.P.5
-
73
-
-
34247844540
-
Aptazyme-based riboswitches as lable-free and detector-free seonsors for cofactors
-
Ogawa, A.; Maeda, M. Aptazyme-based riboswitches as lable-free and detector-free seonsors for cofactors. Bioorg. Med. Chem. Lett. 2007, 17, 3156–3160.
-
(2007)
Bioorg. Med. Chem. Lett
, vol.17
, pp. 3156-3160
-
-
Ogawa, A.1
Maeda, M.2
-
74
-
-
38849166047
-
An artificial aptazyme-based riboswitch and its cascading system in
-
Ogawa, A.; Maeda, M. An artificial aptazyme-based riboswitch and its cascading system in E. coli. ChemBioChem 2008, 9, 206–209.
-
(2008)
E. Coli. Chembiochem
, vol.9
, pp. 206-209
-
-
Ogawa, A.1
Maeda, M.2
-
75
-
-
84890902769
-
Controlling mammalian gene expression by allosteric hepatitis virus ribozymes
-
Nomura, Y.; Zhou, L.; Miu, A.; Yokobayashi, Y. Controlling mammalian gene expression by allosteric hepatitis virus ribozymes. ACS Synth. Biol. 2013, 2, 684–689.
-
(2013)
ACS Synth. Biol
, vol.2
, pp. 684-689
-
-
Nomura, Y.1
Zhou, L.2
Miu, A.3
Yokobayashi, Y.4
-
76
-
-
84891008536
-
A widespread self-cleaving ribozyme class is revealed by bioinformatics
-
Roth, A.; Weinberg, Z.; Chen, A.G.Y.; Kim, P.B.; Ames, T.D.; Breaker, R.R. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat. Chem. Biol. 2014, 10, 56–60.
-
(2014)
Nat. Chem. Biol
, vol.10
, pp. 56-60
-
-
Roth, A.1
Weinberg, Z.2
Chen, A.G.Y.3
Kim, P.B.4
Ames, T.D.5
Breaker, R.R.6
-
77
-
-
84989182979
-
Twister ribozymes a highly versatile expression platforms for artificial riboswitches
-
Felletti, M.; Wurmthaler, L.A.; Geiger, S.; Hartig, J.S. Twister ribozymes a highly versatile expression platforms for artificial riboswitches. Nat. Commun. 2016, 7, 12834.
-
(2016)
Nat. Commun
, vol.7
, Issue.1
-
-
Felletti, M.1
Wurmthaler, L.A.2
Geiger, S.3
Hartig, J.S.4
-
78
-
-
75549088409
-
NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
-
Turner, D.H.; Mathews, D.H. NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. 2010, 38, 280–282.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 280-282
-
-
Turner, D.H.1
Mathews, D.H.2
-
79
-
-
0024477261
-
On finding all suboptimal foldings of an RNA molecule
-
Zuker, M. On finding all suboptimal foldings of an RNA molecule. Science 1989, 244, 48–52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
80
-
-
84934438960
-
UNAFold: Software for Nucleic Acid Folding and Hybridization
-
Keith, J.M., Ed.; Humana Press: Totowa, NJ, USA
-
Markham, N.R.; Zuker, M. UNAFold: Software for Nucleic Acid Folding and Hybridization. In Bioinformatics: Structure, Function and Applications; Keith, J.M., Ed.; Humana Press: Totowa, NJ, USA, 2008; pp. 3–31.
-
(2008)
Bioinformatics: Structure, Function and Applications
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
81
-
-
34249772381
-
Fast Folding and Comparison of RNA Secondary Structures
-
Hofacker, I.L.; Fontana, W.; Stadler, P.F.; Bonhoeffer, L.S.; Tacker, M.; Schuster, P. Fast Folding and Comparison of RNA Secondary Structures. Monatsh. Chem. 1994, 125, 167–188.
-
(1994)
"');">
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
82
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz, R.; Bernhart, S.H.; Höner zu Siederdissen, C.; Tafer, H.; Flamm, C.; Stadler, P.F.; Hofacker, I.L. ViennaRNA Package 2.0. Alg. Mol. Biol. 2011, 6, 26.
-
(2011)
Alg. Mol. Biol
, vol.6
, pp. 26
-
-
Lorenz, R.1
Bernhart, S.H.2
Höner Zu Siederdissen, C.3
Tafer, H.4
Flamm, C.5
Stadler, P.F.6
Hofacker, I.L.7
-
83
-
-
84856397817
-
Analysis of energy-based algorithms for RNA secondary structure prediction
-
Hajiaghayi, M.; Condon, A.; Hoos, H.H. Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinform. 2012, 13, 22.
-
(2012)
BMC Bioinform
, vol.13
, pp. 22
-
-
Hajiaghayi, M.1
Condon, A.2
Hoos, H.H.3
-
84
-
-
84880856064
-
The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective
-
Rivas, E. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. RNA Biol. 2013, 10, 1185–1196.
-
(2013)
RNA Biol
, vol.10
, pp. 1185-1196
-
-
Rivas, E.1
-
85
-
-
84908555190
-
The determination of RNA folding nearest neighbor parameters
-
Andronescu, M.; Condon, A.; Turner, D.H.; Mathews, D.H. The determination of RNA folding nearest neighbor parameters. Methods Mol. Biol. 2014, 1097, 45–70.
-
(2014)
Methods Mol. Biol
, vol.1097
, pp. 45-70
-
-
Andronescu, M.1
Condon, A.2
Turner, D.H.3
Mathews, D.H.4
-
86
-
-
0025264854
-
The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure
-
McCaskill, J.S. The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers 1990, 29, 1105–1119.
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
87
-
-
3042735602
-
Prediction of hybridization and melting for double-stranded nucleic acids
-
Dimitrov, R.A.; Zuker, M. Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J. 2004, 87, 215–226.
-
(2004)
Biophys. J.
, vol.87
, pp. 215-226
-
-
Dimitrov, R.A.1
Zuker, M.2
-
88
-
-
33744979613
-
Partition Function and Base Pairing Probabilities of RNA Heterodimers
-
Bernhart, S.H.; Tafer, H.; Mückstein, U.; Flamm, C.; Stadler, P.F.; Hofacker, I.L. Partition Function and Base Pairing Probabilities of RNA Heterodimers. Algorithms Mol. Biol. 2006, 1, 3.
-
(2006)
Algorithms Mol. Biol
, vol.1
, pp. 3
-
-
Bernhart, S.H.1
Tafer, H.2
Mückstein, U.3
Flamm, C.4
Stadler, P.F.5
Hofacker, I.L.6
-
89
-
-
33847609597
-
Thermodynamic Analysis of Interacting Nucleic Acid Strands
-
Dirks, R.M.; Bois, J.S.; Schaeffer, J.M.; Winfree, E.; Pierce, N.A. Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM Rev. 2007, 49, 65–88.
-
(2007)
SIAM Rev
, vol.49
, pp. 65-88
-
-
Dirks, R.M.1
Bois, J.S.2
Schaeffer, J.M.3
Winfree, E.4
Pierce, N.A.5
-
90
-
-
33646877072
-
Thermodynamics of RNA-RNA Binding
-
Mückstein, U.; Tafer, H.; Hackermüller, J.; Bernhard, S.B.; Stadler, P.F.; Hofacker, I.L. Thermodynamics of RNA-RNA Binding. Bioinformatics 2006, 22, 1177–1182.
-
(2006)
Bioinformatics
, vol.22
, pp. 1177-1182
-
-
Mückstein, U.1
Tafer, H.2
Hackermüller, J.3
Bernhard, S.B.4
Stadler, P.F.5
Hofacker, I.L.6
-
91
-
-
57249083988
-
IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
-
Busch, A.; Richter, A.S.; Backofen, R. IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008, 24, 2849–2856.
-
(2008)
Bioinformatics
, vol.24
, pp. 2849-2856
-
-
Busch, A.1
Richter, A.S.2
Backofen, R.3
-
92
-
-
66349105749
-
A partition function algorithm for interacting nucleic acid strands
-
Chitsaz, H.; Salari, R.; Sahinalp, S.C.; Backofen, R. A partition function algorithm for interacting nucleic acid strands. Bioinformatics 2009, 25, i365–i373.
-
(2009)
Bioinformatics
, vol.25
, pp. i365-i373
-
-
Chitsaz, H.1
Salari, R.2
Sahinalp, S.C.3
Backofen, R.4
-
93
-
-
70349984002
-
Partition Function and Base Pairing Probabilities for RNA-RNA Interaction Prediction
-
Huang, F.W.D.; Qin, J.; Reidys, C.M.; Stadler, P.F. Partition Function and Base Pairing Probabilities for RNA-RNA Interaction Prediction. Bioinformatics 2009, 25, 2646–2654.
-
(2009)
Bioinformatics
, vol.25
, pp. 2646-2654
-
-
Huang, F.W.D.1
Qin, J.2
Reidys, C.M.3
Stadler, P.F.4
-
94
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
-
Xia, T.; SantaLucia, J., Jr.; Burkard, M.E.; Kierzek, R.; Schroeder, S.J.; Jiao, X.; Cox, C.; Turner, D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 1998, 37, 14719–14735.
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.1
Santalucia, J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.6
Cox, C.7
Turner, D.H.8
-
95
-
-
84885805331
-
Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics
-
Elloumi, M., Küng, J., Linial, M., Murphy, R.F., Schneider, K., Toma, C.T., Eds.; Springer: Berlin, Germany, 2008
-
Mückstein, U.; Tafer, H.; Bernhard, S.H.; Hernandez-Rosales, M.; Vogel, J.; Stadler, P.F.; Hofacker, I.L. Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. In BioInformatics Research and Development—BIRD 2008; Elloumi, M., Küng, J., Linial, M., Murphy, R.F., Schneider, K., Toma, C.T., Eds.; Springer: Berlin, Germany, 2008; Volume 13, pp. 114–127.
-
Bioinformatics Research and Development—BIRD 2008
, vol.13
, pp. 114-127
-
-
Mückstein, U.1
Tafer, H.2
Bernhard, S.H.3
Hernandez-Rosales, M.4
Vogel, J.5
Stadler, P.F.6
Hofacker, I.L.7
-
96
-
-
85007493448
-
RNA Folding with Hard and Soft Constraints
-
Lorenz, R.; Hofacker, I.L.; Stadler, P.F. RNA Folding with Hard and Soft Constraints. Algorithms Mol. Biol. 2016, 11, 8.
-
(2016)
Algorithms Mol. Biol
, vol.11
, pp. 8
-
-
Lorenz, R.1
Hofacker, I.L.2
Stadler, P.F.3
-
97
-
-
13444305211
-
The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA Mechanism: A Quantitative Model
-
Hackermüller, J.; Meisner, N.C.; Auer, M.; Jaritz, M.; Stadler, P.F. The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA Mechanism: A Quantitative Model. Gene 2005, 345, 3–12.
-
(2005)
Gene
, vol.345
, pp. 3-12
-
-
Hackermüller, J.1
Meisner, N.C.2
Auer, M.3
Jaritz, M.4
Stadler, P.F.5
-
98
-
-
0034021259
-
RNA folding kinetics at elementary step resolution
-
Flamm, C.; Fontana, W.; Hofacker, I.; Schuster, P. RNA folding kinetics at elementary step resolution. RNA 2000, 6, 325–338.
-
(2000)
RNA
, vol.6
, pp. 325-338
-
-
Flamm, C.1
Fontana, W.2
Hofacker, I.3
Schuster, P.4
-
99
-
-
0025878210
-
The computer simulation of RNA folding involving pseudoknot formation
-
Gultyaev, A.P. The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Res. 1991, 19, 2489–2494.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 2489-2494
-
-
Gultyaev, A.P.1
-
100
-
-
0001742061
-
Activation-energy landscape for metastable RNA folding
-
Fernández, A.; Shakhnovich, E.I. Activation-energy landscape for metastable RNA folding. Phys. Rev. A 1990, 42, 3657–3659.
-
(1990)
Phys. Rev. A
, vol.42
, pp. 3657-3659
-
-
Fernández, A.1
Shakhnovich, E.I.2
-
101
-
-
0027219835
-
A kinetic model of RNA folding
-
Mironov, A.A.; Lebedev, V.F. A kinetic model of RNA folding. Biosystems 1993, 30, 49–56.
-
(1993)
Biosystems
, vol.30
, pp. 49-56
-
-
Mironov, A.A.1
Lebedev, V.F.2
-
102
-
-
0028230845
-
Statistics of RNA Melting Kinetics
-
Tacker, M.; Fontana, W.; Stadler, P.F.; Schuster, P. Statistics of RNA Melting Kinetics. Eur. Biophys. J. 1994, 23, 29–38.
-
(1994)
Eur. Biophys. J
, vol.23
, pp. 29-38
-
-
Tacker, M.1
Fontana, W.2
Stadler, P.F.3
Schuster, P.4
-
103
-
-
84855269212
-
Cotranscriptional folding kinetics of ribonucleic acid secondary structures
-
Zhao, P.; Zhang, W.; Chen, S.J. Cotranscriptional folding kinetics of ribonucleic acid secondary structures. J. Chem. Phys. 2011, 135, doi:10.1063/1.3671644.
-
(2011)
J. Chem. Phys
, vol.135
-
-
Zhao, P.1
Zhang, W.2
Chen, S.J.3
-
104
-
-
84897912844
-
Analysing RNA-kinetics based on folding space abstraction
-
Huang, J.; Voß, B. Analysing RNA-kinetics based on folding space abstraction. BMC Bioinform. 2014, 15, 60.
-
(2014)
BMC Bioinform
, vol.15
, pp. 60
-
-
Huang, J.1
Voß, B.2
-
105
-
-
2442687677
-
Exact Folding Dynamics of RNA Secondary Structures
-
Wolfinger, M.T.; Svrcek-Seiler, W.A.; Flamm, C.; Hofacker, I.L.; Stadler, P.F. Exact Folding Dynamics of RNA Secondary Structures. J. Phys. A Math. Gen. 2004, 37, 4731–4741.
-
(2004)
J. Phys. a Math. Gen
, vol.37
, pp. 4731-4741
-
-
Wolfinger, M.T.1
Svrcek-Seiler, W.A.2
Flamm, C.3
Hofacker, I.L.4
Stadler, P.F.5
-
106
-
-
0033080745
-
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures
-
Wuchty, S.; Fontana, W.; Hofacker, I.L.; Schuster, P. Complete Suboptimal Folding of RNA and the Stability of Secondary Structures. Biopolymers 1999, 49, 145–165.
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
107
-
-
84907487651
-
Memory-efficient RNA energy landscape exploration
-
Mann, M.; Kucharík, M.; Flamm, C.; Wolfinger, M.T. Memory-efficient RNA energy landscape exploration. Bioinformatics 2014, 30, 2584–2591.
-
(2014)
Bioinformatics
, vol.30
, pp. 2584-2591
-
-
Mann, M.1
Kucharík, M.2
Flamm, C.3
Wolfinger, M.T.4
-
108
-
-
0032739568
-
The lid method for exhaustive exploration of metastable states of complex systems
-
Sibani, P.; van der Pas, R.; Schön, J.C. The lid method for exhaustive exploration of metastable states of complex systems. Comput. Phys. Commun. 1999, 116, 17–27.
-
(1999)
Comput. Phys. Commun
, vol.116
, pp. 17-27
-
-
Sibani, P.1
Van Der Pas, R.2
Schön, J.C.3
-
109
-
-
0002631097
-
Valley Structures in the phase space of a finite 3D Ising spin glass with I interactions
-
Klotz, T.; Kobe, S. “Valley Structures” in the phase space of a finite 3D Ising spin glass with I interactions. J. Phys. A Math. Gen. 1994, 27, L95–L100.
-
(1994)
J. Phys. a Math. Gen.
, vol.27
, pp. LL95-L100
-
-
Klotz, T.1
Kobe, S.2
-
110
-
-
0000672765
-
Evolution of the potential energy surface with size for Lennard-Jones clusters
-
Doye, J.P.; Miller, M.A.; Welsh, D.J. Evolution of the potential energy surface with size for Lennard-Jones clusters. J. Chem. Phys. 1999, 111, 8417–8429.
-
(1999)
J. Chem. Phys
, vol.111
, pp. 8417-8429
-
-
Doye, J.P.1
Miller, M.A.2
Welsh, D.J.3
-
111
-
-
0033200608
-
Energy Landscapes, supergraphs, and “folding funnels” in spin systems
-
Garstecki, P.; Hoang, T.; Cieplak, M. Energy Landscapes, supergraphs, and “folding funnels” in spin systems. Phys. Rev. E 1999, 60, 3219–3226.
-
(1999)
Phys. Rev. E
, vol.60
, pp. 3219-3226
-
-
Garstecki, P.1
Hoang, T.2
Cieplak, M.3
-
112
-
-
0036340121
-
Barrier Trees of Degenerate Landscapes
-
Flamm, C.; Hofacker, I.L.; Stadler, P.F.; Wolfinger, M.T. Barrier Trees of Degenerate Landscapes. Z. Phys. Chem. 2002, 216, 155–173.
-
(2002)
Z. Phys. Chem
, vol.216
, pp. 155-173
-
-
Flamm, C.1
Hofacker, I.L.2
Stadler, P.F.3
Wolfinger, M.T.4
-
113
-
-
84904010364
-
Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
-
Kucharík, M.; Hofacker, I.L.; Stadler, P.F.; Qin, J. Basin Hopping Graph: A computational framework to characterize RNA folding landscapes. Bioinformatics 2014, 30, 2009–2017.
-
(2014)
Bioinformatics
, vol.30
, pp. 2009-2017
-
-
Kucharík, M.1
Hofacker, I.L.2
Stadler, P.F.3
Qin, J.4
-
114
-
-
85031505195
-
Tractable Kinetics of RNA—Ligand Interaction
-
Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A., Eds.; Springer: Berlin, Germany
-
Kühnl, F.; Stadler, P.F.; Will, S. Tractable Kinetics of RNA—Ligand Interaction. In Bioinformatics Research and Applications: 12th International Symposium, ISBRA 2016; Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A., Eds.; Springer: Berlin, Germany, 2016; Volume 9683, pp. 337–338.
-
(2016)
Bioinformatics Research and Applications: 12Th International Symposium, ISBRA 2016
, vol.9683
, pp. 337-338
-
-
Kühnl, F.1
Stadler, P.F.2
Will, S.3
-
115
-
-
85031499890
-
Tractable Analysis of RNA—Ligand Interaction Kinetics
-
Kühnl, F.; Stadler, P.F.; Will, S. Tractable Analysis of RNA—Ligand Interaction Kinetics. BMC Bioinform. 2017, in press.
-
(2017)
BMC Bioinform
-
-
Kühnl, F.1
Stadler, P.F.2
Will, S.3
-
116
-
-
77953637928
-
BarMap: RNA Folding on Dynamics Energy Landscapes
-
Hofacker, I.L.; Flamm, C.; Heine, C.; Wolfinger, M.T.; Scheuermann, G.; Stadler, P.F. BarMap: RNA Folding on Dynamics Energy Landscapes. RNA 2010, 16, 1308–1316.
-
(2010)
RNA
, vol.16
, pp. 1308-1316
-
-
Hofacker, I.L.1
Flamm, C.2
Heine, C.3
Wolfinger, M.T.4
Scheuermann, G.5
Stadler, P.F.6
-
117
-
-
84871928528
-
-objective genetic algorithm for pseudoknotted RNA sequence design
-
Multi
-
Taneda, A. Multi-objective genetic algorithm for pseudoknotted RNA sequence design. Front. Genet. 2012, 3, 36.
-
(2012)
Front. Genet
, vol.3
, pp. 36
-
-
Taneda, A.1
-
118
-
-
85028724882
-
RNAblueprint: Flexible multiple target nucleic acid sequence design
-
Hammer, S.; Tschiatschek, B.; Flamm, C.; Hofacker, I.L.; Findeiß, S. RNAblueprint: Flexible multiple target nucleic acid sequence design. Bioinformatics 2017, in press.
-
(2017)
Bioinformatics
-
-
Hammer, S.1
Tschiatschek, B.2
Flamm, C.3
Hofacker, I.L.4
Findeiß, S.5
-
119
-
-
0035257394
-
Design of multistable RNA molecules
-
Flamm, C.; Hofacker, I.L.; Maurer-Stroh, S.; Stadler, P.F.; Zehl, M. Design of multistable RNA molecules. RNA 2001, 7, 254–265.
-
(2001)
RNA
, vol.7
, pp. 254-265
-
-
Flamm, C.1
Hofacker, I.L.2
Maurer-Stroh, S.3
Stadler, P.F.4
Zehl, M.5
-
120
-
-
84909963314
-
Toehold Switches: De-Novo-Designed Regulators of Gene Expression
-
Green, A.A.; Silver, P.A.; Collins, J.J.; Yin, P. Toehold Switches: De-Novo-Designed Regulators of Gene Expression. Cell 2014, 159, 925–939.
-
(2014)
Cell
, vol.159
, pp. 925-939
-
-
Green, A.A.1
Silver, P.A.2
Collins, J.J.3
Yin, P.4
-
121
-
-
84959368267
-
Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
-
Espah-Borujeni, A.; Mishler, D.M.; Wang, J.; Huso, W.; Salis, H.M. Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Res. 2016, 44, 1–13.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. 1-13
-
-
Espah-Borujeni, A.1
Mishler, D.M.2
Wang, J.3
Huso, W.4
Salis, H.M.5
-
122
-
-
84925462732
-
Creating small transcription activating RNAs
-
Chappell, J.; Takahashi, M.K.; Lucks, J.B. Creating small transcription activating RNAs. Nat. Chem. Biol. 2015, 11, 214–220.
-
(2015)
Nat. Chem. Biol
, vol.11
, pp. 214-220
-
-
Chappell, J.1
Takahashi, M.K.2
Lucks, J.B.3
-
123
-
-
85019112209
-
Applicability of a computational design approach for synthetic riboswitches
-
Domin, G.; Findeiß, S.; Wachsmuth, M.; Will, S.; Stadler, P.F.; Mörl, M. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res. 2017, 45, 4108–4119.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. 4108-4119
-
-
Domin, G.1
Findeiß, S.2
Wachsmuth, M.3
Will, S.4
Stadler, P.F.5
Mörl, M.6
-
124
-
-
84890327325
-
Engineering modular ‘ON’ RNA switches using biological components
-
Ceres, P.; Trausch, J.J.; Batey, R.T. Engineering modular ‘ON’ RNA switches using biological components. Nucleic Acids Res. 2013, 41, 10449–10461.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 10449-10461
-
-
Ceres, P.1
Trausch, J.J.2
Batey, R.T.3
-
125
-
-
84882622399
-
Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices
-
Ceres, P.; Garst, A.D.; Marcano-Velázquez, J.G.; Batey, R.T. Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices. ACS Synth. Biol. 2013, 2, 463–472.
-
(2013)
ACS Synth. Biol
, vol.2
, pp. 463-472
-
-
Ceres, P.1
Garst, A.D.2
Marcano-Velázquez, J.G.3
Batey, R.T.4
-
126
-
-
84948112011
-
Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies
-
Meyer, S.; Chappell, J.; Sankar, S.; Chew, R.; Lucks, J.B. Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnol. Bioeng. 2016, 113, 216–225.
-
(2016)
Biotechnol. Bioeng
, vol.113
, pp. 216-225
-
-
Meyer, S.1
Chappell, J.2
Sankar, S.3
Chew, R.4
Lucks, J.B.5
-
127
-
-
33846929128
-
Encoding folding paths of RNA switches
-
Xayaphoummine, A.; Viasnoff, V.; Harlepp, S.; Isambert, H. Encoding folding paths of RNA switches. Nucleic Acids Res. 2006, 35, 614–622.
-
(2006)
Nucleic Acids Res
, vol.35
, pp. 614-622
-
-
Xayaphoummine, A.1
Viasnoff, V.2
Harlepp, S.3
Isambert, H.4
-
128
-
-
84879681227
-
Characterization of 582 natural and synthetic terminators and quantification of their design constraints
-
Chen, Y.J.; Liu, P.; Nielsen, A.A.K.; Brophy, J.A.N.; Clancy, K.; Peterson, T.; Voigt, C.A. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat. Methods 2013, 10, 659–664.
-
(2013)
Nat. Methods
, vol.10
, pp. 659-664
-
-
Chen, Y.J.1
Liu, P.2
Nielsen, A.A.K.3
Brophy, J.A.N.4
Clancy, K.5
Peterson, T.6
Voigt, C.A.7
-
129
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis, H.M.; Mirsky, E.A.; Voigt, C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27, 946–950.
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
131
-
-
84895827954
-
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
-
Borujeni, A.E.; Channarasappa, A.S.; Salis, H.M. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res. 2013, 42, 2646–2659.
-
(2013)
Nucleic Acids Res
, vol.42
, pp. 2646-2659
-
-
Borujeni, A.E.1
Channarasappa, A.S.2
Salis, H.M.3
-
132
-
-
84903163650
-
A family of synthetic riboswitches adopts a kinetic trapping mechanism
-
Mishler, D.M.; Gallivan, J.P. A family of synthetic riboswitches adopts a kinetic trapping mechanism. Nucleic Acids Res. 2014, 42, 6753–6761.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 6753-6761
-
-
Mishler, D.M.1
Gallivan, J.P.2
|