메뉴 건너뛰기




Volumn 3, Issue 2, 2012, Pages 87-91

Synthetic in vitro transcription circuits

Author keywords

DNA nanotechnology; Molecular computing; Synthetic biology; Transcription networks

Indexed keywords

RIBONUCLEASE; RIBONUCLEASE H; RNA POLYMERASE;

EID: 84862730526     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.19734     Document Type: Review
Times cited : (8)

References (35)
  • 1
    • 0029037739 scopus 로고
    • Protein molecules as computational elements in living cells
    • PMID:7630396
    • Bray D. Protein molecules as computational elements in living cells. Nature 1995; 376:307-312. PMID:7630396; http://dx.doi.org/10.1038/376307a0.
    • (1995) Nature , vol.376 , pp. 307-312
    • Bray, D.1
  • 2
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • PMID:11967538
    • Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002; 31:64-68. PMID:11967538; http://dx.doi.org/10.1038/ng881.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 3
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • PMID:10659857
    • Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000; 403:339-342. PMID:10659857; http://dx.doi.org/10.1038/35002131.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 4
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • PMID:10659856
    • Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000; 403:335-38. PMID:10659856; http://dx.doi.org/10.1038/35002125.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 5
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: From modules to systems
    • PMID:19461664
    • Purnick PEM, Weiss R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 2009; 10:410-422. PMID:19461664; http://dx.doi.org/10.1038/nrm2698.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 410-422
    • Purnick, P.E.M.1    Weiss, R.2
  • 6
    • 39149113411 scopus 로고    scopus 로고
    • Modular cell biology: Retroactivity and insulation
    • PMID:18277378
    • Del Vecchio D, Ninfa AJ, Sontag ED. Modular cell biology: retroactivity and insulation. Mol Syst Biol 2008; 4:161. PMID:18277378; http://dx.doi.org/10.1038/msb4100204.
    • (2008) Mol Syst Biol , vol.4 , pp. 161
    • Del Vecchio, D.1    Ninfa, A.J.2    Sontag, E.D.3
  • 7
    • 79951497643 scopus 로고    scopus 로고
    • Computational design approaches and tools for synthetic biology
    • PMID:21258712
    • MacDonald JT, Barnes C, Kitney RI, Freemont PS, Stan GBV. Computational design approaches and tools for synthetic biology. Integr Biol (Camb) 2011; 3:97-108. PMID:21258712; http://dx.doi.org/10.1039/c0ib00077a.
    • (2011) Integr Biol (Camb) , vol.3 , pp. 97-108
    • Macdonald, J.T.1    Barnes, C.2    Kitney, R.I.3    Freemont, P.S.4    Stan, G.B.V.5
  • 8
    • 0242268453 scopus 로고    scopus 로고
    • Principles of cell-free genetic circuit assembly
    • PMID:14559971
    • Noireaux V, Bar-Ziv R, Libchaber A. Principles of cell-free genetic circuit assembly. Proc Natl Acad Sci USA 2003; 100:12672-12677. PMID:14559971; http://dx.doi.org/10.1073/pnas.2135496100
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12672-12677
    • Noireaux, V.1    Bar-Ziv, R.2    Libchaber, A.3
  • 9
    • 79251480753 scopus 로고    scopus 로고
    • Coarse-grained dynamics of protein synthesis in a cell-free system
    • PMID:21405367
    • Karzbrun E, Shin J, Bar-Ziv RH, Noireaux V. Coarse-grained dynamics of protein synthesis in a cell-free system. Phys Rev Lett 2011; 106:048104. PMID:21405367; http://dx.doi.org/10.1103/PhysRevLett.106.048104.
    • (2011) Phys Rev Lett , vol.106 , pp. 048104
    • Karzbrun, E.1    Shin, J.2    Bar-Ziv, R.H.3    Noireaux, V.4
  • 10
    • 0015935359 scopus 로고
    • Characterization of T7-specific ribonucleic acid polymerase. 1. General properties of the enzymatic reaction and the template specificity of the enzyme
    • PMID:4570474
    • Chamberlin M, Ring J. Characterization of T7-specific ribonucleic acid polymerase. 1. General properties of the enzymatic reaction and the template specificity of the enzyme. J Biol Chem 1973; 248:2235-2244. PMID:4570474.
    • (1973) J Biol Chem , vol.248 , pp. 2235-2244
    • Chamberlin, M.1    Ring, J.2
  • 11
    • 0023198428 scopus 로고
    • Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters
    • PMID:3300768
    • Martin CT, Coleman JE. Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters. Biochemistry 1987; 26:2690-2696. PMID:3300768; http://dx.doi.org/10.1021/bi00384a006
    • (1987) Biochemistry , vol.26 , pp. 2690-2696
    • Martin, C.T.1    Coleman, J.E.2
  • 12
    • 0035854429 scopus 로고    scopus 로고
    • Interrupting the template strand of the T7 promoter facilitates translocation of the DNA during initiation, reducing transcript slippage and the release of abortive products
    • PMID:11439019
    • Jiang M, Rong M, Martin C, McAllister WT. Interrupting the template strand of the T7 promoter facilitates translocation of the DNA during initiation, reducing transcript slippage and the release of abortive products. J Mol Biol 2001; 310:509-522. PMID:11439019; http://dx.doi.org/10.1006/jmbi.2001.4793.
    • (2001) J Mol Biol , vol.310 , pp. 509-522
    • Jiang, M.1    Rong, M.2    Martin, C.3    McAllister, W.T.4
  • 13
  • 14
    • 79952998426 scopus 로고    scopus 로고
    • Nucleic acid based molecular devices
    • PMID:21432950
    • Krishnan Y, Simmel FC. Nucleic acid based molecular devices. Angew Chem Int Ed Engl 2011; 50:3124-3156. PMID:21432950; http://dx.doi.org/10.1002/anie.200907223.
    • (2011) Angew Chem Int Ed Engl , vol.50 , pp. 3124-3156
    • Krishnan, Y.1    Simmel, F.C.2
  • 15
    • 0037169502 scopus 로고    scopus 로고
    • Substitution of ribonucleotides in the T7 RNA polymerase promoter element
    • PMID:11704669
    • McGinness KE, Joyce GF. Substitution of ribonucleotides in the T7 RNA polymerase promoter element. J Biol Chem 2002; 277:2987-2991. PMID:11704669; http://dx.doi.org/10.1074/jbc.M108820200.
    • (2002) J Biol Chem , vol.277 , pp. 2987-2991
    • McGinness, K.E.1    Joyce, G.F.2
  • 16
    • 67149138163 scopus 로고    scopus 로고
    • Protein sequestration generates a flexible ultrasensitive response in a genetic network
    • Buchler NE, Cross FR. Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol Syst Biol 2009; 5:272; http://dx.doi.org/10.1038/msb.2009.30
    • (2009) Mol Syst Biol , vol.5 , pp. 272
    • Buchler, N.E.1    Cross, F.R.2
  • 17
    • 0015851235 scopus 로고
    • Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid-deoxyribonucleic acid hybrid structures
    • PMID:4580046
    • Berkower I, Leis J, Hurwitz J. Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid-deoxyribonucleic acid hybrid structures. J Biol Chem 1973; 248:5914-5921. PMID:4580046.
    • (1973) J Biol Chem , vol.248 , pp. 5914-5921
    • Berkower, I.1    Leis, J.2    Hurwitz, J.3
  • 18
    • 0030735085 scopus 로고    scopus 로고
    • Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1
    • PMID:9346880
    • Lima WF, Crooke ST. Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1. J Biol Chem 1997; 272:27513-27516. PMID:9346880; http://dx.doi.org/10.1074/jbc.272.44.27513
    • (1997) J Biol Chem , vol.272 , pp. 27513-27516
    • Lima, W.F.1    Crooke, S.T.2
  • 20
    • 33846116559 scopus 로고    scopus 로고
    • Construction of an in vitro bistable circuit from synthetic transcriptional switches
    • PMID:17170763
    • Kim J, White KS, Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol 2006; 2:68. PMID:17170763; http://dx.doi.org/10.1038/msb4100099
    • (2006) Mol Syst Biol , vol.2 , pp. 68
    • Kim, J.1    White, K.S.2    Winfree, E.3
  • 21
    • 79551599731 scopus 로고    scopus 로고
    • Synthetic in vitro transcriptional oscillators
    • PMID:21283141
    • Kim J, Winfree E. Synthetic in vitro transcriptional oscillators. Mol Syst Biol 2011; 7:465. PMID:21283141; http://dx.doi.org/10.1038/msb.2010.119
    • (2011) Mol Syst Biol , vol.7 , pp. 465
    • Kim, J.1    Winfree, E.2
  • 22
    • 0034212551 scopus 로고    scopus 로고
    • Engineering stability in gene networks by autoregulation
    • PMID:10850721
    • Becskei A, Serrano L. Engineering stability in gene networks by autoregulation. Nature 2000; 405:590-593. PMID:10850721; http://dx.doi.org/10.1038/35014651
    • (2000) Nature , vol.405 , pp. 590-593
    • Becskei, A.1    Serrano, L.2
  • 23
    • 0034633702 scopus 로고    scopus 로고
    • Generation of oscillations by the p53- Mdm2 feedback loop: A theoretical and experimental study
    • PMID:11016968
    • Lev Bar-Or R, Maya R, Segel LA, Alon U, Levine AJ, Oren M. Generation of oscillations by the p53- Mdm2 feedback loop: a theoretical and experimental study. Proc Natl Acad Sci USA 2000; 97:11250-1125. PMID:11016968; http://dx.doi.org/10.1073/pnas.210171597
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 11250-11255
    • Lev, B.-O.R.1    Maya, R.2    Segel, L.A.3    Alon, U.4    Levine, A.J.5    Oren, M.6
  • 24
    • 28844502722 scopus 로고    scopus 로고
    • Circadian clocks-the fall and rise of physiology
    • PMID:16341082
    • Roenneberg T, Merrow M. Circadian clocks-the fall and rise of physiology. Nat Rev Mol Cell Biol 2005; 6:965-971. PMID:16341082; http://dx.doi.org/10.1038/nrm1766
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 965-971
    • Roenneberg, T.1    Merrow, M.2
  • 25
    • 0038241770 scopus 로고    scopus 로고
    • Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
    • PMID:12787501
    • Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 2003; 113:597-607. PMID:12787501; http://dx.doi.org/10.1016/S0092-8674(03)00346-5
    • (2003) Cell , vol.113 , pp. 597-607
    • Atkinson, M.R.1    Savageau, M.A.2    Myers, J.T.3    Ninfa, A.J.4
  • 26
    • 80053650824 scopus 로고    scopus 로고
    • Timing molecular motion and production with a synthetic transcriptional clock
    • PMID:21921236
    • Franco E, Friedrichs E, Kim J, Jungmann R, Murray R, Winfree E, et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc Natl Acad Sci USA 2011; 108:784-793. PMID:21921236; http://dx.doi.org/10.1073/pnas.1100060108
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 784-793
    • Franco, E.1    Friedrichs, E.2    Kim, J.3    Jungmann, R.4    Murray, R.5    Winfree, E.6
  • 27
    • 0023924749 scopus 로고
    • Processivity in early stages of transcription by T7 RNA polymerase
    • PMID:3415967
    • Martin CT, Muller DK, Coleman JE. Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry 1988; 27:3966-3974. PMID:3415967; http://dx.doi.org/10.1021/bi00411a012
    • (1988) Biochemistry , vol.27 , pp. 3966-3974
    • Martin, C.T.1    Muller, D.K.2    Coleman, J.E.3
  • 28
    • 79251621970 scopus 로고    scopus 로고
    • Dynamic DNA nanotechnology using strand-displacement reactions
    • PMID:21258382
    • Zhang DY, Seelig G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 2011; 3:103-113. PMID:21258382; http://dx.doi.org/10.1038/nchem.957
    • (2011) Nat Chem , vol.3 , pp. 103-113
    • Zhang, D.Y.1    Seelig, G.2
  • 29
    • 79957946108 scopus 로고    scopus 로고
    • Scaling up digital circuit computation with DNA strand displacement cascades
    • PMID:21636773
    • Qian L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 2011; 332:1196-1201. PMID:21636773; http://dx.doi.org/10.1126/science.1200520
    • (2011) Science , vol.332 , pp. 1196-1201
    • Qian, L.1    Winfree, E.2
  • 30
    • 37849051357 scopus 로고    scopus 로고
    • Networking particles over distance using oligonucleotide-based devices
    • PMID:18031039
    • Yashin R, Rudchenko S, Stojanovic MN. Networking particles over distance using oligonucleotide-based devices. J Am Chem Soc 2007; 129:15581-15584. PMID:18031039; http://dx.doi.org/10.1021/ja074335t
    • (2007) J Am Chem Soc , vol.129 , pp. 15581-15584
    • Yashin, R.1    Rudchenko, S.2    Stojanovic, M.N.3
  • 31
    • 79551586208 scopus 로고    scopus 로고
    • Programming an in vitro DNA oscillator using a molecular networking strategy
    • PMID:21283142
    • Montagne K, Plasson R, Sakai Y, Fujii T, Rondelez Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol Syst Biol 2011; 7:466. PMID:21283142.
    • (2011) Mol Syst Biol , vol.7 , pp. 466
    • Montagne, K.1    Plasson, R.2    Sakai, Y.3    Fujii, T.4    Rondelez, Y.5
  • 32
    • 67650666435 scopus 로고    scopus 로고
    • Modelling amorphous computations with transcription networks
    • PMID:19474083
    • Simpson ZB, Tsai TL, Nguyen N, Chen X, Ellington AD. Modelling amorphous computations with transcription networks. J R Soc Interface 2009; 6:523-533. PMID:19474083; http://dx.doi.org/10.1098/rsif.2009.0014.focus
    • (2009) J R Soc Interface , vol.6 , pp. 523-533
    • Simpson, Z.B.1    Tsai, T.L.2    Nguyen, N.3    Chen, X.4    Ellington, A.D.5
  • 33
    • 33846095183 scopus 로고    scopus 로고
    • Neural network computation by in vitro transcriptional circuits
    • Kim J, Hopfield JJ, Winfree E. Neural network computation by in vitro transcriptional circuits. Adv Neural Inf Process Syst 2004; 17:681-688.
    • (2004) Adv Neural Inf Process Syst , vol.17 , pp. 681-688
    • Kim, J.1    Hopfield, J.J.2    Winfree, E.3
  • 34
    • 67650666435 scopus 로고    scopus 로고
    • Modelling amorphous computations with transcription networks
    • PMID:19474083
    • Simpson ZB, Tsai TL, Nguyen N, Chen X, Ellington AD. Modelling amorphous computations with transcription networks. J R Soc Interface 2009; 6:523-533; http://dx.doi.org/10.1098/rsif.2009.0014.focus; PMID:19474083
    • (2009) J R Soc Interface , vol.6 , pp. 523-533
    • Simpson, Z.B.1    Tsai, T.L.2    Nguyen, N.3    Chen, X.4    Ellington, A.D.5
  • 35
    • 84855481443 scopus 로고    scopus 로고
    • Competition for catalytic resources alters biological network dynamics
    • PMID:22304295
    • Rondelez Y. Competition for catalytic resources alters biological network dynamics. Phys Rev Lett 2012; 108:018102. PMID:22304295; http://dx.doi.org/10.1103/PhysRevLett.108.018102
    • (2012) Phys Rev Lett , vol.108 , pp. 018102
    • Rondelez, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.