메뉴 건너뛰기




Volumn 30, Issue 11, 2012, Pages 1137-1142

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

Author keywords

[No Author keywords available]

Indexed keywords

CONTEXT EFFECTS; GENETIC PROGRAMS; INPUT-OUTPUT; RIBOZYMES; SYNTHETIC GENES; TEMPORAL CONTROLS; UNTRANSLATED REGIONS;

EID: 84869476328     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2401     Document Type: Article
Times cited : (296)

References (48)
  • 1
    • 0242490792 scopus 로고    scopus 로고
    • Limitations of quantitative gene regulation models: A case study
    • Kim, P.M. & Tidor, B. Limitations of quantitative gene regulation models: A case study. Genome Res. 13, 2391-2395 (2003
    • (2003) Genome Res , vol.13 , pp. 2391-2395
    • Kim, P.M.1    Tidor, B.2
  • 2
    • 39149113411 scopus 로고    scopus 로고
    • Modular cell biology: Tetroactivity and insulation
    • Del Vecchio, D., Ninfa, A.J. & Sontag, E.D. Modular cell biology: Tetroactivity and insulation. Mol. Syst. Biol. 4, 161 (2008
    • (2008) Mol. Syst. Biol , vol.4 , pp. 161
    • Del Vecchio, D.1    Ninfa, A.J.2    Sontag, E.D.3
  • 3
    • 77952473769 scopus 로고    scopus 로고
    • Strategies for protein synthetic biology
    • Grünberg, R. & Serrano, L. Strategies for protein synthetic biology. Nucleic Acids Res. 38, 2663-2675 (2010
    • (2010) Nucleic Acids Res , vol.38 , pp. 2663-2675
    • Grünberg, R.1    Serrano, L.2
  • 4
    • 70350324632 scopus 로고    scopus 로고
    • Emergent bistability by a growth-modulating positive feedback circuit
    • Tan, C., Marguet, P. & You, L. Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 5, 842-848 (2009
    • (2009) Nat. Chem. Biol , vol.5 , pp. 842-848
    • Tan, C.1    Marguet, P.2    You, L.3
  • 5
    • 66149172363 scopus 로고    scopus 로고
    • Diversity-based model-guided construction of synthetic gene networks with predicted functions
    • Ellis, T., Wang, X. & Collins, J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 27, 465-471 (2009
    • (2009) Nat. Biotechnol , vol.27 , pp. 465-471
    • Ellis, T.1    Wang, X.2    Collins, J.J.3
  • 6
    • 34547916832 scopus 로고    scopus 로고
    • Environmental signal integration by a modular and gate
    • Anderson, J.C., Voigt, C.A. & Arkin, A.P. Environmental signal integration by a modular AND gate. Mol. Syst. Biol. 3, 133 (2007
    • (2007) Mol. Syst. Biol , vol.3 , pp. 133
    • Anderson, J.C.1    Voigt, C.A.2    Arkin, A.P.3
  • 7
    • 80055035853 scopus 로고    scopus 로고
    • Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
    • Wang, B., Kitney, R.I., Joly, N. & Buck, M. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun. 2, 508 (2011
    • (2011) Nat. Commun , vol.2 , Issue.508
    • Wang, B.1    Kitney, R.I.2    Joly, N.3    Buck, M.4
  • 8
    • 14844358192 scopus 로고    scopus 로고
    • Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
    • Hooshangi, S., Thiberge, S. & Weiss, R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. USA 102, 3581-3586 (2005
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 3581-3586
    • Hooshangi, S.1    Thiberge, S.2    Weiss, R.3
  • 9
    • 15544388848 scopus 로고    scopus 로고
    • Noise propagation in gene networks
    • Pedraza, J.M. & van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965-1969 (2005
    • (2005) Science , vol.307 , pp. 1965-1969
    • Pedraza, J.M.1    Van Oudenaarden, A.2
  • 10
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • Endy, D. Foundations for engineering biology. Nature 438, 449-453 (2005
    • (2005) Nature , vol.438 , pp. 449-453
    • Endy, D.1
  • 11
    • 33748953866 scopus 로고    scopus 로고
    • Genetic parts to program bacteria
    • Voigt, C.A. Genetic parts to program bacteria. Curr. Opin. Biotechnol. 17, 548-557 (2006
    • (2006) Curr. Opin. Biotechnol , vol.17 , pp. 548-557
    • Voigt, C.A.1
  • 12
    • 33744509927 scopus 로고    scopus 로고
    • Engineering life: Building a fab for biology
    • Bio FAB Group et al
    • Bio FAB Group et al. Engineering life: Building a fab for biology. Sci. Am. 294, 44-51 (2006
    • (2006) Sci. Am. , vol.294 , pp. 44-51
  • 13
    • 45149118469 scopus 로고    scopus 로고
    • Jr Engineering BioBrick vectors from BioBrick parts
    • Shetty, R.P., Endy, D. & Knight, T.F. Jr Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2, 5 (2008
    • (2008) J. Biol. Eng , vol.2 , pp. 5
    • Shetty, R.P.1    Endy, D.2    Knight, T.F.3
  • 14
    • 77649305316 scopus 로고    scopus 로고
    • BglBricks: A flexible standard for biological part assembly
    • Anderson, J.C. et al. BglBricks: A flexible standard for biological part assembly. J. Biol. Eng. 4, 1 (2010
    • (2010) J. Biol. Eng , vol.4 , Issue.1
    • Anderson, J.C.1
  • 15
    • 77956652264 scopus 로고    scopus 로고
    • Programming cells: Towards an automated 'Genetic Compiler'
    • Clancy, K. & Voigt, C.A. Programming cells: Towards an automated 'Genetic Compiler'. Curr. Opin. Biotechnol. 21, 572-581 (2010
    • (2010) Curr. Opin. Biotechnol , vol.21 , pp. 572-581
    • Clancy, K.1    Voigt, C.A.2
  • 16
    • 46949110597 scopus 로고    scopus 로고
    • Setting the standard in synthetic biology
    • Arkin, A. Setting the standard in synthetic biology. Nat. Biotechnol. 26, 771-774 (2008
    • (2008) Nat. Biotechnol , vol.26 , pp. 771-774
    • Arkin, A.1
  • 17
    • 84860155171 scopus 로고    scopus 로고
    • Predicting the strength of UP-elements and full-length E. coli σe promoters
    • 10.1093/nar/gkr1190
    • R hodius, V.A., Mutalik, V.K. & Gross, C.A. Predicting the strength of UP-elements and full-length E. coli σE promoters. Nucleic Acids Res. 10.1093/nar/gkr1190 (2012
    • (2012) Nucleic Acids Res.
    • Rhodius, V.A.1    Mutalik, V.K.2    Gross, C.A.3
  • 18
    • 79951565301 scopus 로고    scopus 로고
    • Design, construction and characterization of a set of insulated bacterial promoters
    • Davis, J.H., Rubin, A.J. & Sauer, R.T. Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 39, 1131-1141 (2011
    • (2011) Nucleic Acids Res , vol.39 , pp. 1131-1141
    • Davis, J.H.1    Rubin, A.J.2    Sauer, R.T.3
  • 19
    • 0031554704 scopus 로고    scopus 로고
    • Engineering mRNA stability in E. coli by the addition of synthetic hairpins using a 5 cassette system
    • Carrier, T.A. & Keasling, J.D. Engineering mRNA stability in E. coli by the addition of synthetic hairpins using a 5 cassette system. Biotechnol. Bioeng. 55, 577-580 (1997
    • (1997) Biotechnol. Bioeng , vol.55 , pp. 577-580
    • Carrier, T.A.1    Keasling, J.D.2
  • 20
    • 84867389802 scopus 로고    scopus 로고
    • RNA processing enables predictable programming of gene expression
    • advance online publication doi:10.1038/nbt.235516 September 2012
    • Qi, L., Haurwitz, R.E., Shao, W., Doudna, J.A. & Arkin, A.P. RNA processing enables predictable programming of gene expression. Nat. Biotechnol. advance online publication, doi:10.1038/nbt.2355 (16 September 2012
    • Nat. Biotechnol
    • Qi, L.1    Haurwitz, R.E.2    Shao, W.3    Doudna, J.A.4    Arkin, A.P.5
  • 21
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner, T.S., Cantor, C.R. & Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342 (2000
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 22
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz, M.B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (2000
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 24
    • 77949405661 scopus 로고    scopus 로고
    • Synthesizing a novel genetic sequential logic circuit: A push-on push-off switch
    • Lou, C. et al. Synthesizing a novel genetic sequential logic circuit: A push-on push-off switch. Mol. Syst. Biol. 6, 350 (2010
    • (2010) Mol. Syst. Biol , vol.6 , Issue.350
    • Lou, C.1
  • 25
    • 0030861452 scopus 로고    scopus 로고
    • And tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements
    • Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25, 1203-1210 (1997
    • (1997) Nucleic Acids Res , vol.25 , pp. 1203-1210
    • Lutz, R.1    Independent, B.H.2
  • 26
    • 18344411608 scopus 로고
    • Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing
    • Buzayan, J.M., Gerlach, W.L. & Bruening, G. Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing. Proc. Natl. Acad. Sci. USA 83, 8859-8862 (1986
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 8859-8862
    • Buzayan, J.M.1    Gerlach, W.L.2    Bruening, G.3
  • 28
    • 0023643095 scopus 로고
    • Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site
    • Forster, A.C. & Symons, R.H. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50, 9-16 (1987
    • (1987) Cell , vol.50 , pp. 9-16
    • Forster, A.C.1    Symons, R.H.2
  • 29
    • 0030860475 scopus 로고    scopus 로고
    • A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities
    • Di Serio, F., Daròs, J.A., Ragozzino, A. & Flores, R. A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities. J. Virol. 71, 6603-6610 (1997
    • (1997) J. Virol , vol.71 , pp. 6603-6610
    • Di Serio, F.1    Daròs, J.A.2    Ragozzino, A.3    Flores, R.4
  • 30
    • 0023684191 scopus 로고
    • Nucleotide sequence predicts circularity and self-cleavage of 300-ribonucleotide satellite of arabis mosaic virus
    • Kaper, J.M., Tousignant, M.E. & Steger, G. Nucleotide sequence predicts circularity and self-cleavage of 300-ribonucleotide satellite of arabis mosaic virus. Biochem. Biophys. Res. Commun. 154, 318-325 (1988
    • (1988) Biochem. Biophys. Res. Commun , vol.154 , pp. 318-325
    • Kaper, J.M.1    Tousignant, M.E.2    Steger, G.3
  • 31
    • 0026538051 scopus 로고
    • Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures
    • Hernández, C. & Flores, R. Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proc. Natl. Acad. Sci. USA 89, 3711-3715 (1992
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 3711-3715
    • Hernández, C.1    Flores, R.2
  • 33
    • 79961137158 scopus 로고    scopus 로고
    • Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks
    • Beal, J., Lu, T. & Weiss, R. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS ONE 6, e22490 (2011
    • (2011) PLoS ONE 6, e22490
    • Beal, J.1    Lu, T.2    Weiss, R.3
  • 34
    • 84859641038 scopus 로고    scopus 로고
    • Using gene expression noise to understand gene regulation
    • Munsky, B., Neuert, G. & van Oudenaarden, A. Using gene expression noise to understand gene regulation. Science 336, 183-187 (2012
    • (2012) Science , vol.336 , pp. 183-187
    • Munsky, B.1    Neuert, G.2    Van Oudenaarden, A.3
  • 35
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361 (1977
    • (1977) J. Phys. Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 36
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
    • Arkin, A., Ross, J. & McAdams, H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics 149, 1633-1648 (1998
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 37
    • 33751347484 scopus 로고    scopus 로고
    • The finite state projection algorithm for the solution of the chemical master equation
    • Munsky, B. & Khammash, M. The finite state projection algorithm for the solution of the chemical master equation. J. Chem. Phys. 124, 044104 (2006
    • (2006) J. Chem. Phys , vol.124 , pp. 044104
    • Munsky, B.1    Khammash, M.2
  • 38
    • 73149105740 scopus 로고    scopus 로고
    • Listening to the noise: Random fluctuations reveal gene network parameters
    • Munsky, B., Trinh, B. & Khammash, M. Listening to the noise: Tandom fluctuations reveal gene network parameters. Mol. Syst. Biol. 5, 318 (2009
    • (2009) Mol. Syst. Biol , vol.5 , pp. 318
    • Munsky, B.1    Trinh, B.2    Khammash, M.3
  • 40
    • 66149144779 scopus 로고    scopus 로고
    • A stochastic spectral analysis of transcriptional regulatory cascades
    • Walczak, A.M., Mugler, A. & Wiggins, C.H. A stochastic spectral analysis of transcriptional regulatory cascades. Proc. Natl. Acad. Sci. USA 106, 6529-6534 (2009
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 6529-6534
    • Walczak, A.M.1    Mugler, A.2    Wiggins, C.H.3
  • 41
    • 33645870422 scopus 로고    scopus 로고
    • Production of the antimalarial drug precursor artemisinic acid in engineered yeast
    • Ro, D.-K. et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940-943 (2006
    • (2006) Nature , vol.440 , pp. 940-943
    • Ro, D.-K.1
  • 42
    • 84860803588 scopus 로고    scopus 로고
    • Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca
    • Temme, K., Zhao, D. & Voigt, C.A. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc. Natl. Acad. Sci. USA 109, 7085-7090 (2012
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 7085-7090
    • Temme, K.1    Zhao, D.2    Voigt, C.A.3
  • 43
    • 77649254204 scopus 로고    scopus 로고
    • Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE
    • R hodius, V.A. & Mutalik, V.K. Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc. Natl. Acad. Sci. USA 107, 2854-2859 (2010
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 2854-2859
    • Rhodius, V.A.1    Mutalik, V.K.2
  • 44
    • 70349964350 scopus 로고    scopus 로고
    • 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. 27, 946-950 (2009
    • (2009) Nat. Biotechnol , vol.27 , pp. 946-950
    • Salis, H.M.1    Mirsky, E.A.2    Voigt, C.A.3
  • 46
    • 66149143984 scopus 로고    scopus 로고
    • Measuring the activity of BioBrick promoters using an in vivo reference standard
    • Kelly, J.R. et al. Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng.3, 4 (2009
    • (2009) J. Biol. Eng. , vol.3 , Issue.4
    • Kelly, J.R.1
  • 47
    • 0043009734 scopus 로고    scopus 로고
    • Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
    • Khvorova, A., Lescoute, A., Westhof, E. & Jayasena, S.D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10, 708-712 (2003
    • (2003) Nat. Struct. Biol , vol.10 , pp. 708-712
    • Khvorova, A.1    Lescoute, A.2    Westhof, E.3    Jayasena, S.D.4
  • 48
    • 27644432146 scopus 로고    scopus 로고
    • Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants
    • Nelson, J.A., Shepotinovskaya, I. & Uhlenbeck, O.C. Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants. Biochemistry 44, 14577-14585 (2005
    • (2005) Biochemistry , vol.44 , pp. 14577-14585
    • Nelson, J.A.1    Shepotinovskaya, I.2    Uhlenbeck, O.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.